You will have a wealth of choices. Aside from super remote locales, most ryokans offer ground transfer services from the nearest train station. To keep things simple, I'll limit your options to places that are within a 2 hour train ride with no transfers. From Tokyo, Hakone (Gora Kadan, Yama No Chaya, Gora Hanaougi, Hakone Ginyu), Nikko (Fufu Nikko) and Izu (Asaba, Yagyu no Sho, Ufufu, Abba Resorts Izu Zangyoso) are good options. Another option is Fukushima (city), which is just 90 minutes from Tokyo Station to Fukushima Station via the Yamagata Shinkansen (Onyado Kawasemi is a very nice ryokan there.) Kyoto offers less options. Kaga Onsen (Beniya Mukayu, Kayotei) is probably your best bet. From there, you can take a short trip to Kanazawa (about an hour by train) and check out the sights there (definitely recommended.) There are some great sightseeing spots and ryokans in Gunma (Kusatsu Onsen), Gifu (Takayama, Gero) and large parts of Nagano, but many of those places are less convenient to get to (and take more time.)