I would second the Shingawa Prince Hotel. Nice place in a great location (right across from Shinagawa station, a huge transportation hub).
If you want something cheaper (~$80/night) and more "Japanese", but more off the beaten path, there's a ryokan (traditional Japanese inn) near Nippori station called the
Katsutarou Annex. They speak English..or at least one of them does. It's still on the Yamanote train line, same as Shinagawa, Shibuya, Shinjuku, Ikebukuro etc. and is in a neat location, though not as convenient as Shinagawa.