If you're not sure where to spend the night(s) when you come to Tokyo, Yawp! is the best place you can wish for.
My friend and I spent ten days in Tak's guesthouse, and we couldn't recommend it enough. His place is conveniently situated, near the station and a couple of stores where you can get food from.
The guesthouse is quite cosy, and the beds are very confy. Of course, it gets a bit noisier than in a hotel at times, but the experience is totally worth it.
Tak is a super friendly host, he showed us a lot of great places to visit and to eat in around the city and the neighborhood. We actually had dinner and drinks with him and other guests, every other night or so.
Thanks again for everything, Tak !