Yoshimi & Marek's place is a little gem. We felt that we had a really authentic experience of Tokyo staying in their apartment. The neighbourhood is peaceful and access to the subway is easy so you can do all the hotspots without too much hassle and retreat to a calm location at night.
The apartment has everything that you need and the aircons work beautifully on hot Tokyo evenings. The beds are ridiculously comfy.
There are some really great supermarkets at Oshiage Station as well as a Ghibli store - big highlight for my family as we are avid fans. All in all a great spot from which to explore a very memorable city.