Hello again Jay,
If only taking what you are interested into consideration, Kyoto could be the best option for more traditional/historical sites (there are many: https://www.accessible-japan.com/wheelchair-accessible-travel-destinations-and-tourist-attractions-in-kyoto/), while Tokyo has more modern innovations.
That being said, you can find very nice examples of traditional attractions even in Tokyo. If you want to see some traditional arts in Tokyo check out The Kabukiza Theater (very cool with audio interpretation) or the National Noh Theater, if you want some shrines then there is Sensoji, Nezu Jinja, or the lovely Meiji Jingu (more here: https://www.accessible-japan.com/wheelchair-accessible-travel-destinations-and-tourist-attractions-in-tokyo/), and if you like museums definitely check out the Ueno Park Museum.
Some things to consider, the closet airport to Kyoto is in Osaka, from there hauling your luggage will require going on a train and/or vehicle to a hotel in Kyoto. There are some options near stations in Kyoto so it may not be too much of an issue from the train but I can’t say for sure. Many of the attractions I visited in Kyoto are level and easy to get around, however, some like Kiyomizu-dera are a bit of a trek and even has a pretty steep hill at one part.
Getting to destinations in Kyoto will rely on bus, taxi, or car if not more walking. The train/metro system in Kyoto isn’t super extensive, while in Tokyo you can get near most places solely by them.
If you want to carry less luggage, look for a place with laundry facilities. I did this when I stayed in a “Weekly Mansion” (essentially an apartment building turn into hotel rental) in Osaka, so at the end of the first week we did some laundry at the machines on the first floor.
Lastly, if you have access to, and can use, a manual wheelchair (or maybe a collapsible power assisted wheelchair, preferably not a scooter) then you may want consider using it. You’ll find many places willing to help you if they can. For example, station staff will help getting you on the right trains.
I hope that helps,