The most convenient area as accommodation in Tokyo would be Shinjuku or Shibuya. There are tons of restaurants and convenience stores, also has multiple train lines so it's easy to go to anywhere.
East of Tokyo has more traditional atmosphere such as Asakusa and Ueno if you prefer more atmosphere. There are some ryokan (traditional Japanese inns) in Asakusa, too if you are interested in staying in a tatami room.
I don't know very well about Kyoto and Osaka so I'll leave the answer to someone else.