Homeikan is a fantastic place to stay in Tokyo. It is a beautiful old traditional Japanese inn, all wooden, very unusual. The staff are excellent. and the rooms very comfortable, all with tatami mats, and a lot of character. The only drawbacks are that there are shared bathrooms, in the Japanese style, and the walls are thin, so if anyone near you is being noisy at night, you do hear it.
Stayed at Homeikan, Tokyo