I'd recommend http://www.kimiryokan.jp/
any day. The owner takes aikido as well.
It's traditional japanese ryokan. You share the showers and bathrooms, but it's clean, relatively cheap and very nice (in my opinion).
Also it is in walking distance from Ikebukoro station from where you can get to most interesting places in Tokyo Area. I'd also recommend a one or two night stay in Hakone with a swift trip up the volcano.. it's really nice.
Have a great trip