My preference for winter visit would be Kyoto, Noto Hanto, Kamakura and Nikko. I visited winter Kyoto as a teenager and it was devoid of the dusty feeling of a summer visit. All the gardens have this extra cleanliness and tranquility.

Noto Hanto is good for winter as the Kenrokuen garden in Kanasawa is famous for snow scenes. All the trees are supported for heavy snow. Many locals visit in traditional garb for photo sessions. At the hotels and ryokans especially in Wakuraonsen, you can enjoy outdoor pool while the snow is falling. Winter is also the season for local kani (crab) and usually breakfast and dinner are included in the room charge.

Kamakura visit in the winter will give you much more elbow room and the shops and restaurants will have more time for you. The beach at Enoshima will be free of vendors and return to its natural state until next spring.

The upper lake area of both Nikko and Hakone will be too cold but the lower valleys should still be reasonable. Of the two, Nikko have much more to see on foot.