I am such a strong proponent of recreational train riding in Japan that Ifm going to sound like a broken record, but that sort of activity sounds like a natural match for your situation. One of my favorite things to do in Japan is to take scenic train rides, and they are certainly very easy on the legs. My typical pattern is to keep a given hotel for multiple days (up to a week) and take long-distance day trips where I leave in the morning, take a pleasant train ride somewhere, do a little carefully planned sightseeing (not too much) at the destination, and return in the mid- to late afternoon. If I had mobility issues, I would pick a hotel that is directly connected to a JR station (this is also helpful when it rains), and I would probably pick sightseeing venues that were easily accessibly by cab from the destination JR Station, and that had loaner wheelchairs available.
If you like Japanese gardens, for example, Kenrokuen in Kanazawa would be a viable destination from Tokyo. There are parts of the grounds that are not wheelchair accessible, but they do have a designated loop, and they apparently have loaner wheelchairs. That could be a swell day trip. (Buy good food to eat on the train in both directions.) The scenery on the Hokuriku shinkansen is a mixed bag (some tunnels) but if you havenft seen it, it would be interesting. (Between Nagano and Kanazawa is particularly good.) Another good day would be Ritsurin Koen in Takamatsu, coming from Osaka, Okayama, or even Kyoto. (That garden is a little more accessible.)
One of the best day trips I ever took was an excursion to Adachi Museum in Yasugi, when I was staying in Okayama as a home base (there are numerous other good train-riding day trips from that city as well). The train ride is particularly scenic, and the museum is quite wheelchair friendly. The gardens are viewed from inside the museum so they are of course wheelchair friendly as well.
Have you visited the Accessible Japan website? I canft exactly vouch for it because I havenft used it, but I have seen it mentioned numerous times. You didnft mention whether you were willing to use wheelchairs, but if it were me, I would. Ifm afraid that there arenft that many things you can do in Japan that donft involve at least a little walking plus a lot of being on your feet.
https://www.accessible-japan.com/ Donft overlook museums (of many, many kinds), aquariums, and possibly sporting events. A baseball game in Japan can be quite an experience. Or I suppose therefs sumo or something (Ifm definitely not a fan), or traditional types of theatre.