Jørgen Jakob Friis
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
Thanks for the link Jørgen. I met Minato-san a few times, and I planned to stay at his place the next time I was in Tokyo.
For those who aren't familiar with Tokyo geography, it's not all that close to Hombu, but it is only a short train ride, and Minato-san will help you out with finding your way around.