largest city: Tokyo / prefectures: Gunma, Tochigi, Ibaraki, Saitama, Chiba, Tokyo and Kanagawa
If you are looking for hiking or trailing not so far from Tokyo, Oze national park is the place where you should go.
Yokohama, the second most populous city in Japan is a harbor city approximately 30 minutes train ride from Tokyo. The biggest Chinatown in Japan is located in Yokohama too.
If you are interested in railway related tourist attraction which can be reached within a day trip from Tokyo, probably Usui No.3 railway bridge is the place to visit.
Tokyo is not just a megalopolis with skyscrapers. There are wonderful gardens too. If you have a day in Tokyo, why not visit Shinjuku-gyoen national garden during the day?