Stay in Minatomirai
One of the nicest hotels are Pan Pacific and Intercontinental Hotel in Yokohama, Japan. Although not in Tokyo, it is right smack in the middle of Minatomirai, a district with a breathtaking night view and amazing experiences. From these hotels, you can easily access any of the main facilities/buildings/sightseeing spots of Yokohama, such as Minatonomieru Okakouen, Motomachi, Cosmo World, World Porters, shopping areas in Yokohama and more. Furthermore, because it is so close to the Minatomirai and Sakuragicho Stations, you can easily go to Shibuya, Shinjuku, Roppongi, Kamakura, Enoshima, Ginza, etc.
These are probably the best hotels you can go to, if you want easy accessibility, a beautiful view and a relatively relaxing area at night.