I go to Japan every year or so for a couple of weeks. I usually stay in Ikebukuro in Tokyo.
As Ikebukuro is a major subway/train station, you can be just about anywhere in Tokyo in 30 minutes such as Akihabara or Shinjuku.
There is a great inn there called the Kimi Ryokan which is Japanese styled and foreigner friendly.
Moreover, the rate for a single room is $45.00 a night. Can't beat it.
http://www.kimi-ryokan.jp/