Capsule hotels are definitely a good option, often the bunks in a shared room of a hostel are set up in a similar style and give about the same amount of space anyway.
These hostels are fairly good in Asakusa:
http://kshouse.jp/tokyo-oasis-e/
http://retrometrobackpackers.com/index-en.html
This ryokan in Ikebukuro is nice:
http://www.kimiryokan.jp/
cheers