When my wife's parents come to visit us in Tokyo they stay across the street from us at the
Dormy Inn Hatchobori- the rooms are typical Japanese small but they are fine -- and they love the "Onsen" that is at the property as well as being right next to Hatchobori Station which allows easy access to multiple lines -- or you can easily walk to Ginza or enjoy a walk on the Sumida River. Prices are always reasonable (for Tokyo lol) and it's clean and well kept. Plenty of decent restaurants as well (which is one of the many reasons we live in the neighborhood).