Mt. Fuji is one of most popular spots. Because it is the highest mountain in Japan and very accessible from Tokyo. It is about 2 hours away from Shinjuku, Tokyo by the train or the express bus. You can visit there as a day trip from Tokyo easily.
In this post, I would like to show you several trip plan to Fuji Five Lakes area which includes Mt. Fuji 5th station. When you go to Mt. Fuji, Lake Kawaguchi (Kawaguchiko) is the gateway. I also will show you the access to Lake Kawaguchi.
Access to Lake Kawaguchi and Fujisan area
Lake Kawaguchi (Kawaguchiko) is the hub in this area. Most buses depart from Kawaguchiko station. You can get there by either the train or the express bus. I will show you the acesse route to Kawaguchiko first of all.
Access to Lake Kawaguchi from Tokyo
There are many routes available to get Lake Kawaguchi but these are mostly by the express bus. If you take the train, you will depart from Shinjuku or Tokyo.
Before choosing the route, you have to make sure which pass you will use or do not use any passes. The route is varied by the pass. I would like to show you the best and most cost efficient way.
Train access to Kawaguchiko (Lake Kawaguchi) from Shinjuku via Otsuki by JR Pass or JR East Pass
You may use JR Pass or JR East Pass in your trip. In this case, the limited express Fuji Kaiyu (Fuji Excursion) is the best choice. This train takes you to Kawaguchiko directly. There is only two scheduled round trips a day. And this train has been very popular and hard to book a seat. But on the some specific dates, there is one or two extra trips. Please find the timetable in JR East official site in the link below:
JR East official site – the timetable
When you cannot take this train, you can take the limited express Azusa or Kaiji between Shinjuku and Otsuki. And you have to change the trains at Otsuki and take Fuji Kyuko Railway to Kawaguchiko.
Fuji Kyuko Railway between Otsuki and Kawaguchiko is not covered by either JR pass or JR East Pass. Please find the fare for Otsuki to/from Kawaguchiko in Fuji Kyuko Railway official site:
Fuji Kyuko Railway official site
Fuji Kyuko railway ticket can be purchased at some JR station. When you book a seat for the limited express train from Shinjuku to Kawaguchiko or Otsuki by JR pass or JR East pass, you may ask the staff to purchase a ticket for Fuji Kyuko Railway. You may be able to buy it. If you cannot, you can purchase it at Otsuki station or pay when you exit Kawaguchiko station or pay to the conductor on board.
The typical trip schedule is the following:
Shinjuku (1 hour by the limited express Azusa or Kaiji) Otsuki (50 minutes by the limited express train / 60 minutes by the local train) Kawaguchiko
The train access to Kawaguchiko (Lake Kawaguchi) from Shinjuku via Otsuki by Tokyo Wide Pass
You can take same route as JR Pass and JR East Pass above. But Tokyo Wide Pass covers all the way to Kawaguchiko which includes Fuji Kyuko Railway segment between Otsuki and Kawaguchiko. The extra cost is not required to take Fuji Kyuko Railway.
Access to Lake Kawaguchi from many locations in Tokyo by bus
Actually the express bus is most convenient way. The express bus depart from Shinjuku, Shibuya, Tokyo, and both Haneda and Narita airports. It is faster than train. And the biggest benefit by the express bus is direct transfer. If you take a train, you have to change the trains at Otsuki. But if you take the express bus, you can get Kawaguchiko (Lake Kawaguchi) station, Fujisan station, Fuji-Q Highland, even Fuji 5th station (seasonal), Oshino-Hakkai and Lake Yamanaka directly.
Typical trip schedule is the following:
Shinjuku (1 hour 45 minutes by Express Bus) Kawaguchiko
Seasonally you can get 5th station directly too. If you do not intend to use any train passes, simply pay regular fare to take express bus. Any rail passes do not cover this express bus. You can find the information in Fujikyu Bus official site:
Fujikyu Bus – Highway Bus Information
Access to Lake Kawaguchi from Hakone by bus
If you intend to visit Lake Kawaguchi before/after visiting Hakone, you can catch the bus between Kawaguchiko station, Fuji-Q Highland, Fujisan station, Gotemba station and Gotemba Premium Outlet. Please see the link below to find more information:
You may find some information about Hakone in the link below:
Access from Osaka, Kyoto and Nagoya. How to add Lake Kawaguchi on the way to Tokyo
The gateway to Lake Kawaguchi area from Osaka, Kyoto and Nagoya is Mishima. You can catch the express bus which is called Mishima/Kawaguchiko Liner Express Bus between Mishima and Lake Kawaguchi, Fuji-Q Highland, Fujisan station. Please see the link below to find the information about the bus from Mishima.
Fujikyu Bus – Highway Bus Information
You can get Mishima by the Shinkansen from Nagoya, Kyoto and Shin-Osaka. Some Hikari which is the second fastest train stop at Mishima. Please check the timetable of the Shinkansen in the link below:
JR Central official site – The Tokaido and the Sanyo Shinkansen timetable
Please refer the post below to find some more information about Mishima station. You can find the information about the transfer between the Shinkansen and the bus to Kawaguchiko:
Sample itineraries to visit Mt. Fuji from Lake Kawaguchi to Lake Kawaguchi.
I would like to show you the sample itinerary of Mt. Fuji part only. This sample itinerary is starting from Lake Kawaguchi and finishing at Lake Kawaguchi. You can add one of these sample itineraries on the access route from Tokyo to Lake Kawaguchi or other cities to Lake Kawaguchi.
Lake Kawaguchi and 5th station one day plan
This itinerary includes most popular spots around Lake Kawaguchi area.
Kawaguchiko (Trip time 55 minutes by bus) 5th station
Enjoy mountain air in the middle of Mt. Fuji (1 hour)
5th station (Trip time 55 minutes by bus) Kawaguchiko
Lunch time around Kawaguchiko station
Kawaguchiko (Trip time 15 minutes by Fuji Kyuko Railway train) Shimo-Yoshida
Visit Arakura Fuji Sengen shrine, Chureito Pagoda (1 hour)
Shimo-Yoshida (Trip time 15 minutes by Fuji Kyuko Railway train) Kawaguchiko
Visit Mt. Tenjo Ropeway (Kachi Kachi Yama Ropeway) and/or Cruise on Lake Kawaguchi
*If you start this trip in very early morning, you may visit both.
Lake Kawaguchi and Shibazakura venue one day plan
Fuji Shibazakura Festival is hold from mid April to late May. Shibazakura (pink moss flower) cover the field and Mt. Fuji can be seen behind this amazing pink field. You can find more information in the official site:
Fuji Shibazakura Festival official site
Try to get Shibazakura venue to avoid congestion. This festival is very popular and still getting popular year by year.
Kawaguchiko (Trip time 30 minutes by Shibazakura Liner shuttle bus or 50 minutes by regular bus) Fuji Shibazakura venue
Enjoy Shibazakura Festival (2 hours)
*It usually takes 60 to 90 minutes to see this festival. But you can spend more if you like. And also there are lots of food stands in the venue. These stands offer many kinds of local food. You can take lunch before you leave.
*In the period of this festival, combo ticket which includes round trip bus fare and admission is sold around 2,000 yen. You can purchase it at Kawaguchiko station.
*If you intend to take the express bus from Shinjuku, some of buses are running to Shibazakura venue directly.
Fuji Shibazakura venue (Trip time 30 minutes by Shibazakura Liner shuttle bus or 50 minutes by regular bus) Kawaguchiko
Visit Mt. Tenjo Ropeway (Kachi Kachi Yama Ropeway) and/or Cruise on Lake Kawaguchi
*If you start this trip in very early morning, you may visit both.
You may visit Arakura Fuji Sengen shrine, Chureito Pagoda instead.
Kawaguchiko (Trip time 15 minutes by Fuji Kyuko Railway train) Shimo-Yoshida
Stay for one hour to visit shrine.
Shimo-Yoshida (Trip time 15 minutes by Fuji Kyuko Railway train) Kawaguchiko
If you intend to take a train, you can go back to Tokyo via Otsuki from Shimo-Yoshida. You do not need to go back to Kawaguchiko.
Shibazakura Festival and 5th station one day plan
Try to get Shibazakura venue to avoid congestion. This festival is very popular and still getting popular year by year.
Kawaguchiko (Trip time 30 minutes by Shibazakura Liner shuttle bus or 50 minutes by regular bus) Fuji Shibazakura venue
Enjoy Shibazakura Festival (2 hours)
*It usually takes 60 to 90 minutes to see this festival. But you can spend more if you like. And also there are lots of food stands in the venue. These stands offer many kinds of local food. You can take lunch before you leave. Otherwise you have a lunch time at Kawaguchiko station.
*In the period of this festival, combo ticket which includes round trip bus fare and admission is sold around 2,000 yen. You can purchase it at Kawaguchiko station.
*If you intend to take the express bus from Shinjuku, some of buses are running to Shibazakura venue directly.
Fuji Shibazakura venue (Trip time 30 minutes by Shibazakura Liner shuttle bus or 50 minutes by regular bus) Kawaguchiko (Trip time 55 minutes by bus) 5th station
Enjoy mountain air in the middle of Mt. Fuji (1 hour)
5th station (Trip time 55 minutes by bus) Kawaguchiko
5th station and Fuji-Q highland one day plan
Kawaguchiko (Trip time 55 minutes by bus) 5th station
Enjoy mountain air in the middle of Mt. Fuji (1 hour)
5th station (Trip time 55 minutes by bus) Kawaguchiko (Trip time 3 minutes by Fuji Kyuko Railway train) Fuji-Q Highland
Enjoy Fuji-Q Highland as much as you want. You can have lunch time in either Kawaguchiko or Fuji-Q Highland.
Fuji-Q Highland (Trip time 3 minutes by Fuji Kyuko Railway train) Kawaguchiko
If you intend to take a train, you can go back to Tokyo via Otsuki from Fuji-Q Highland. You do not need to go back to Kawaguchiko.
Mt Fuji overnight 2 days plan
If you can spend 2 days, you can visit most of places in Lake Kawaguchi and surrounding area.
Day 1
Kawaguchiko (Trip time 30 minutes by Shibazakura Liner shuttle bus or 50 minutes by regular bus) Fuji Shibazakura venue
Enjoy Shibazakura Festival (2 hours)
Fuji Shibazakura venue (Trip time 30 minutes by Shibazakura Liner shuttle bus or 50 minutes by regular bus) Kawaguchiko
If you do not visit in spring season, you may visit Oshino-Hakkai instead.
Kawaguchiko (Trip time 25 minutes by regular bus) Oshino-Hakkai
Enjoy walking in Oshino-Hakkai (1.5 to 2 hours)
Oshino-Hakkai (Trip time 25 minutes by regular bus) Kawaguchiko
Lunch time around Kawaguchiko station
Kawaguchiko (Trip time 15 minutes by Fuji Kyuko Railway train) Shimo-Yoshida
Visit Arakura Fuji Sengen shrine, Chureito Pagoda (1 hour)
Shimo-Yoshida (Trip time 15 minutes by Fuji Kyuko Railway train) Kawaguchiko
Visit Mt. Tenjo Ropeway (Kachi Kachi Yama Ropeway) and/or Cruise on Lake Kawaguchi
Stay in Lake Kawaguchi
Day 2
Kawaguchiko (Trip time 55 minutes by bus) 5th station
Enjoy mountain air in the middle of Mt. Fuji (1 hour)
5th station (Trip time 55 minutes by bus) Kawaguchiko (Trip time 3 minutes by Fuji Kyuko Railway train) Fuji-Q Highland
Enjoy Fuji-Q Highland as much as you want. You can have lunch time in either Kawaguchiko or Fuji-Q Highland.
Fuji-Q Highland (Trip time 3 minutes by Fuji Kyuko Railway train) Kawaguchiko
If you intend to take a train, you can go back to Tokyo via Otsuki from Fuji-Q Highland. You do not need to go back to Kawaguchiko.
If you are not interested in Fuji-Q Highland, you can visit museum and park around Lake Kawaguchi. You may take Fujikyu bus to visit various places around Fuji Five Lake. Please find some information in the link below:
Fuji Kyuko Bus official site – Route bus information
I hope this post helps you to build your trip plan to Lake Kawaguchi and Mt. Fuji are.
Comments
Hi takeshi san,
Is that hokuriku arch pass cover this route? :
1. Narita – tokyo by nex (return)
2. Haneda – Hamamatsucho by monorail
3. Ueno – katsuta by ltd.exp hitachi
4. All of JR Line in Tokyo (incl.yamanote line) and kyoto
5. From osaki to odaiba by rinkai line?
Thanks before
Hi Sweetchild san,
1. Yes
2. Yes
3. No
4. Yes
5. No
Cheers,
Takeshi / JPRail.com
Hallo again Takeshi San?
From Tokyo to Kanazawa by hokuriku arch pass, only by shinkansen kagayaki? Or i can board asama and or hakutaka also?
Thank you
Hi Sweetchild san,
Asama does not go to Kanazawa. It runs between Tokyo and Nagano only. You can take either Hakutaka or Kagayaki. But Hakutaka is slower than Kagayaki because it stops many more stations than Kagayaki. Please see the link below to find the timetable:
http://www.eki-net.com/pc/jreast-shinkansen-reservation/english/wb/common/timetable/index.html
Cheers,
Takeshi / JPRail.com
Hi Takeshi / JPRail.com
I’m marshel from Indonesia, am very impressed with the detail itinerary sample that you provided, it’s amazing and very helpful!
I would like to ask your assistance to build an itinerary for 2 days Fuji+hakone trip.
We are planning to go to Japan via Narita airport (arrive on 16Sept 2018), from there we will go directly to Mt. Fuji and stay at Mystays Hotel Fuji-Kawaguci-ko. Please kindly advise me the best itinerary for Fuji and Hakone trip.
We are very keen to go to gotemba, and visit onsen at hakone
Thank you so much in advance.
Hi Marshel,
Please see the link below. You will find two days sample itinerary.
https://jprail.com/sample-itineraries/1to3-days/fuji-and-hakone-two-days-trip-sample-itinerary-spring-version.html
Cheers,
Takeshi / JPRail.com
Hi Takeshi san,
I am visiting Mount fuji area in Oct with my family. I just want to check the route if i were to start from Shinjuku to Lake Kawaguchi and head towards hakone.
I cant find any research on how to get to Hakone from Lake Kawaguchi. Is always Hakone to Lake Kawaguchiko.
Tokyo-Lake Kawaguchi – 1 night
Lake Kawaguchi – Hakone – 1 night
Hakone – Oyama – Tokyo
Do you think 1 night each in sufficient to cover Kawaguchi, 5th station, okawadani and Hakone?
Regards,
Mei Yin
Hi Mei san,
I have a sample itinerary of Fuji and Hakone 2 days. You can find all info which you need in this itinerary:
https://jprail.com/sample-itineraries/1to3-days/fuji-and-hakone-two-days-trip-sample-itinerary-spring-version.html
Cheers,
Takeshi / JRPail.com
Hi takeshi,
i use JR Hokuriku Arch Pass, if i want to go to kawaguchiko is it covered by this pass?
Hi Suad,
Kawaguchiko is not in the coverage area of Hokuriku Arch Pass. I recommend you to take an express bus by regular fare.
Cheers,
Takeshi / JPRail.com
Hello again Takeshi san,
This is my itinerary :
Day 1:
Landing narita and go to hitachi seaside park and go back to hotel ini tokyo.
Day 2:
From tokyo to kawaguchiko and return to tokyo.
Day 3:
Tokyo to Toyama (japan alps one day trip) and return to tokyo
There are so many pass for transfort in japan. I confused to choose one.
Can you give me some advice which pass is better for that itinerary?
Thank you
Hi Sweetchild san,
You may use Hokuriku Arch Pass and Tateyama Kurobe option ticket for day 1 and 3.
https://jprail.com/travel-informations/other-rail-passes/rail-pass-for-visitors/tokyo-osaka-hokuriku-arch-pass-user-guide-clarify-valid-trains-coverage-area-and-compare-single-fare-and-pass.html
http://www.jrtateyama.com/e/
For day 2, just take express bus by regular fare.
Cheers,
Takeshi / JPRail.com
Hi Takeshi san,
Can i use tokyo wide pass to take narita express from and to narita airport?
Hi Sweetchild san,
Yes, you can.
Cheers,
Takeshi / JPRail.com
Dear Takeshi
We are 4 Australians travelling October 2018 to Tokyo. We wish to independently travel to Nikko 26/27/28
29 /30 Hakone
31 Mt Fuji
Nov 1/2 Matsumoto
3/4 Takayama (do the alpine circuit )
5/6 Kanazawa
7/8/9/10/11 Kyoto
12/13 Okayama (day trip to Naoshima)
14/15 Hiroshima & Miyajima
16/17/18/19/20 Kyushu
21 Nagoya/ Nakatsugawa to hike Nakasendo Way on an organised trip which includes transport to the end in Narai
26 Nov we catch a train back to Tokyo before flying out 7-20PM Thursday 29
We are confused about all the available passes which cover each area (Fuji Hakone pass, Nikko Pass ect!!!) or do we get 2 different JR rail passes 21 & 7 day, then pay for the train Narai to Tokyo?
Does the JR pass cover travel around Tokyo or do we need a Suica Pass?
Hi Lorna,
I recommend you to use JR East Pass Nagano Niigata for Nikko, Fuji, Hakone and Matsumoto.
https://jprail.com/travel-informations/other-rail-passes/rail-pass-for-visitors/jr-east-pass-niigata-and-nagano-flex-5-days-pass-in-14-days-period-to-cover-kanto-region-nagano-and-niigata.html
But this pass covers Tokyo to Odawara only when you get Hakone.
https://jprail.com/sample-itineraries/1to3-days/how-to-build-the-trip-plan-to-hakone-various-sample-itineraries-of-hakone.html
And you can restart using this pass at Otsuki if you intend to visit (or stay) in Lake Kawaguchi.
https://jprail.com/sample-itineraries/1to3-days/how-to-build-the-trip-plan-to-fuji-area-various-sample-itineraries-of-fuji-five-lakes-and-5th-station.html
You may access to Matsumoto from Otsuki by this pass.
Use Tateyama Kurobe option ticket for Alpine route:
http://www.jrtateyama.com/e/
Once you get Toyama after alpine route, start using Takayama Hokuriku area pass if you intend to visit Shirakawago too. You can use it until you get Kyoto. If you don’t visit Shirakwago, regular ticket is okay.
https://jprail.com/travel-informations/other-rail-passes/rail-pass-for-visitors/takayama-hokuriku-area-pass-perfect-deal-to-get-takayama-kanazawa-toyama-shirakawago-from-nagoya-or-osaka.html
You can start using JR Pass 21 days when you leave for Okayama. If you don’t use Takayama Hokuriku area pass, you can start using JR pass 21 says when you leave Kanazawa. Single ticket is okay for Takayama and Kanazawa.
Cheers,
Takeshi / JPRail.com
Hi takeshi San
Can I just check is it doable for me to go from shibuya to shibazakura festival and then subsequently to gotemba premium outlet and back to shibuya on the same day?
What are the best cost saying option for me of this is doable?
Is it 1 way direct bus from shibuya to kawaguchiko then transfer to shibazakura 2 way bus then subsequently 1 way bus to gotemba premium outlet and lastly 1 way bus back to shibuya?
Is the itinerary above realistic or to separate the 2 location into 2 days are more realistic?
Thank you
Hi Wendy san,
It’s not impossible. It you take the earliest bus to Kawaguchiko, you can get Shibazakura venue before 10:00 am. There is one direct bus from Shinjuku to Shibazakura venue. If you take the direct bus, you have to pay bus fare and Shibazakura entrance fee one by one.
http://bus-en.fujikyu.co.jp/highway/detail/id/1
You will be back to Kawaguchiko by 13:00. You can catch the bus to outlet at 13:30 and arrive in outlet at 15:00. If you want more time in outlet, try to take a bus from Kawaguchiko at 12:30.
And take a bus to get back to Shinjuku.
https://www.premiumoutlets.co.jp/en/gotemba/access/
Cheers,
Takeshi / JPRail.com
Hi takeshi San,
Thank you for the sharing, meaning I’ll have to book a one way ticket from shinjuku to shibazakura 2200 yen and pay for entrance fee at 600 yen, but is there a 1 way bus from shibazakura to kawaguchiko? I do saw a round trip of 2000 yen on shibazakura website including the entrance fee but I did not see the 1 way fee?
Subsequently I will have to catch another bus from kawaguchiko to gotemba premium outlet and finally from gotemba premium outlet back to shinjuku
Thank you
Hi Wendy,
One fare is available, it’s 1230 yen.
Cheers,
Takeshi / JPRail.com
Hi takeshi San,
Thank you for the info 🙂
No worries, Wendy san.
Cheers,
Takeshi / JPRail.com
Hi Takeshi-san,
I have JR pass and want to go to Lake Kawaguchiko from Yokohama. Not planning to stayover.
Can you advise what route to take if I’m going from West Tokyo (Ueno area)? Thank you so much
Hi Meli san,
You can get Shinjuku by JR Yamanote line or JR Chuo line.
https://jprail.com/travel-informations/tips-for-japan-rail-pass/best-way-efficient-how-much-can-we-use-japan-rail-pass-in-downtown-tokyo.html
After Shinjuku, just follow the route in the post above.
Cheers,
Takeshi / JPRail.com
Dear Takeshi San,
I am planning two days Hakone & Mt Fuji trip between Osaka & Tokyo.
D1 –> Osaka to Odawara (by JR Pass) day trip at Hakone with Fuji Hakone Pass. Stay at Hotel near Gora.
D2 –> Gora to Gotemba to Kawaguchi-ko/ Lake Kawaguchi then back to Shinjuku
Hakone day trip is fine form me, I am confuse on Mt Fuji’s arrangement.
May I know which is the best way back to Shinjuku by JR pass?
Thank you
Regards
Ashley
Hi Ashley san,
You may take Fuji Kyuko railway from Kawaguchiko to Otsuki. And then take Limited Express Azusa or Kaiji from Otsuki.
https://jprail.com/trains/sort-by-type/limited-express/limited-express-azusa-super-azusa-and-kaiji.html
JR pass covers from Otsuki to Shinjuku only. Fuji Hakone Pass covers Kawaguchiko to Shimo-Yoshida. So you need to pay for Shimo-Yoshida to Otsuki which costs around 1000 yen. You can pay this when you get Otsuki station. Just show your Fuji Hakone Pass and JR Pass at Fuji Kyuko railway ticket gate at Otsuki and they will collect the fare.
Cheers,
Takeshi / JPRail.com
Dear Takeshi,
Thanks for your prompt reply.
1) Can I make a reservation seat for Limited Express Azusa or Kaiji in advance when I activate my JR pass? Is it same as reservation seat for shinkansen?
2) The station at Shinjuku referring to Shinjuku JR?
I have a few questions about JR pass shinkansen seat reservation:
3) Once i make reservation, will they issue me a ticket?
4) How to change my reservation?
5) If i miss my reservation time, can i cancel and make another reservation on the spot? (same day later time)
Thank you.
Best Regards
Hi Ashley,
1. Yes. Whenever I use JR pass, I complete all booking when I exchange JR pass.
2. Yes.
3. Yes. The ticket shows date of travel, car number, and seat number.
4. You can return your ticket and rebook it at any major JR stations.
5. Yes, you can. Same procedure as 4 without any penalty.
Cheers,
Takeshi / JPRail.com
Hi Takeshi San,
This is the first time for my family to visit Tokyo and Hokkaido.
We would like to seek your guidance for the transportation, overnights stay and itinerary for both destinations. My schedule are as follows:
1. Arrival Tokyo Haneda Airport: 10th May 2018 at 6.45 am
2. Depart Tokyo Haneda Airport: 17th May 2018 at 9.15 am
Please advise which options is more economical in terms of fare and travelling time from Tokyo to/back from Hokkaido.
A) By bullet train – If this option, is using JR pass better and how many days pass is sufficient. Is luggage allowed in the train
and any restrictions in luggage size/weight/pieces for each passenger.
B) By Domestic Flight-can we book in advance and which airline. Any restrictions in baggage size/weight. Which airport in Hokkaido to check in.
Hokkaido- can you recommend the itinerary, if using the JR pass.
Which place to stay overnight to save travelling time.
Is the JR stations in Hokkaido accessible to all the place of interest within walking distance?
How many days shall I spent in Hokkaido and Tokyo.
We hope to hear from you soon. Thanks for your time.
Best regards,
Lilian
Hi Lilian san,
First of all, I cannot compare flight and train. Because flight fare is varied by the season and occupancy. New Chitose is most common airport near Sapporo. But there are many airports, such as Hakodate, Kushiro, Memabetsu (near Abashiri) in Hokkaido and you can reach most of airport in Hokkaido from Haneda.
If you take a train, please see the link below to find the info about access to Hokkaido.
https://jprail.com/destinations/hokkaido-area/how-to-get-sapporo.html
Basically you can bring the luggage in train without any restriction. But there is no specific space for the luggage. You need to keep it in your seat. Please find more info in the link below:
https://jprail.com/travel-informations/travel-tips/baggage/managing-luggage-how-to-carry-your-baggage-on-board-and-how-to-store-your-baggage-at-the-station.html
Regarding luggage on domestic flight, it depends on the carrier and the flight ticket. Some affordable rate does not include check in baggage fee.
If you see whole part of Hokkaido, even 7 days is not enough. But if you see Sapporo, Otaru, Hakodate and some spots in southern part of Hokkaido, 4 days stay is okay. Please make sure where you go in Hokkaido. Regarding place to stay, it depends on where you stay. If you visit Sapporo and/or Hakodate, you may need to take subway and/or streetcar. Please see the link below to find more info:
https://www.japan-guide.com/list/e1101.html
JR pass or JR East South Hokkaido Rail Pass is your choice. If you visit southern part of Hokkaido only, JR East South Hokkaido Rail Pass is okay. It’s cheaper than JR Pass.
https://jprail.com/destinations/hokkaido-area/jr-east-south-hokkaido-rail-pass-user-guide-perfect-deal-for-the-travelers-who-visit-tokyo-and-sapporo-by-train.html
For the stay in Tokyo, it’s same thing. You have to find where you go first. Otherwise you cannot find how much time you need.
Cheers,
Takeshi / JPRail.com