I don't recommend a capsule hotel. The facilities are geared towards people who stayed out drinking and missed the last train home - not ideal for someone with luggage and several nights to stay. If you're looking for the absolute cheapest stays, I suggest searching this forum and the budget travel forum for backpacker hostels.
For reasonable hotels in the Ueno area, this thread has some good info. :
http://www.flyertalk.com/forum/japan...pori-area.html