The Universal Rooms of Keio Plaza Hotel (Shinjuku) are well designed for wheelchair users. The hotel has a long history of working for the accessibility of their services. The rooms have nice views from the 30th floor, too. Maybe you should check it if it is not on your list. https://www.keioplaza.com/rooms/universal.html

If you want the transport from Narita Airport to hotels in tokyo, a car with a lift costs a bit more. If you stay somewhere in Chiba Pref. it would be less depending the distance from the airport. If you need to find a lift taxi, we will be able to support you. Please contact [email protected].

It may be an option:

Kawaguchiko Station –(Fuji Kyoko Bus)– JR Gotenba Station — (JR Train)–Matsuda Stn. –(walk 3 min.)–Shin-matsuda Stn. –(Odakyu Train) — Odawara Stn. –(Hakone Tozan Train)–…

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There is a bus connecting from Kofu to Kawaguchiko. Their buses are all accessible (can accommodate one wheelchair or two) as far as I checked with the staff today on the phone. It takes 70-80 minutes from the JR Kofu Station to Kawaguchiko Station, 10 buses per day from departure (Kofu Minami Station) at 7:40…

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Both Tokyo Metro and Toei Transportation say all the stations are accesisble.

https://www.tokyometro.jp/safety/barrierfree/progress/tozai/index.html

https://www.kotsu.metro.tokyo.jp/eng/guides/wheelchair/
As for JR train stations in Tokyo 23 Wards, there are a few. You do not need to worry normally.