Isa-san and Yumiko-san's guesthouse is the perfect place to come back to every night after a busy day of exploring Tokyo. The guesthouse really feels like your home—very cozy, peaceful, incredibly clean, beautiful, and has everything you need. Even though the bathroom is shared, it gets cleaned everyday and really feels like a private space. I've also enjoyed getting to know the other guests staying here and having conversations with Isa-san. Also: I highly recommend taking a sushi class with Isa-san, it's really fun!
Kuramae is a nice and peaceful part of the city; there are lots of great coffee shops and restaurants in the area without all the touristy crowds. The guesthouse is right by several metro stops, so it's really easy to get anywhere from there, and it's a direct metro ride from the airport.
I absolutely recommend staying here, and I plan to stay here during my next visit to Tokyo!