This may be a bit of a train ride out from the center of Tokyo but it is well worth it if you're looking for a quiet place to stay for the night, not to mention affordable! Masa was super nice and made sure I knew how to take care of the apartment along with making my way around town.
The surrounding neighborhood is a wonderful walk and the station is only minutes away. The portable wifi included in the price is a definite plus too. It lasts on its own for maybe half a day so make sure to have a battery on hand.