Stay a while in Tokyo
If you want to be in the city for an extended stay the best option is to check out the serviced apartments. An online search for Tokyo Serviced Apartments turns up a myriad of options.
If you're just staying a few days, but don't want to stay in a hotel, check out a vacation rental property. www.airbnb.com lists a few.
If you're on your own one of the "guest houses" may be an option.
What flavor do you want? Urban - stay in the city. Urban without the crowds, somewhere in Saitama may work for you. Urban with some crowds, lots to do, easy access - Kichijoji is a good choice, or Ueno or Ogikubo.