Tokyo is making steps to improve universal access – or bariafurī (barrier free; バリアフリー) in Japanese. It is a slow process, though one that has gotten a boost from the 2020 Olympics preparations. Newer buildings have wheelchair-access ramps, and more and more subway stations have elevators (look for signs on the platform, as not all exits have elevators); train station staff will help you on and off the train with a temporary slope.
A fair number of hotels, from the higher end of midrange and above, offer a barrier-free room or two (book well in advance); note that what constitutes barrier free is not always consistent, so check the details carefully. Larger attractions, train stations, department stores and shopping malls have wheelchair-accessible restrooms. Should you decide upon arrival that a wheelchair (車いす; kuruma isu) is necessary, hotel staff can help you rent one.
Accessible Japan (www.accessible-japan.com) is the best resource; they also produce an ebook with lots of detail.
Download Lonely Planet's free Accessible Travel guide from http://lptravel.to/AccessibleTravel.