HI there, id recomend the Khaosan-tokyo asakusa.
Khaosan Tokyo Asakusa Annex Hostel in Tokyo, Japan
they have a few hostels and are very friendly and excellent value for money.
Capsule hotels id recomend as a last resort, but if youv never tried a capsule before, Its definatly worth doing.
If you get to Kyoto, I reccoment the Diaya Ryokan
Daiya Ryokan Hostel in Kyoto, Japan
id be happy to answer any other questions (provided im not too rusty in my knowledge tho
)