You cannot go wrong with Homeikan. Just right across from Tokyo University. And further off is a park you can row boats at your leisure. Though most of the staff do not speak English (you can't expect them to), you can and the staff can get along just fine. If you are unsure how to use the room, bath,and restrooms just ask and they will happily show you.

Benares
From USA
We stayed at Homeikan, Tokyo