Very much depends on what you are interested in.
But for places with ease of access to most tourist spots in the Kanto region (that's Ibaraki, Tochigi and Chiba, Gunma, Saitama, Tokyo, Kanagawa & Yamanashi Prefectures.) and access to areas such as Kamakura, Mt. Fuji, Shibuya, Ryogoku I'd recommend staying in Shinagawa. The Prince hotel is apparently very good (i've not stayed there as i live in Yokohama). Shinagawa also enables easy access to other areas such as Kyoto.
But once again, it very much depends on your interests. about 6 years ago