Nina and I stayed at this Japanese inn, run by my friend and former climbing partner Michael Turner and his Japanese wife. I figured if I once trusted him with my life, I could trust him for a few nights' sleep.
It's also rather convenient, nearly staring you in the face when you exit one of the stations on the Tozai subway line, and a very short walk from the Takadanobaba station on the JR Yamanote loop around Tokyo.