I've only visited Hokkaido in the winter for skiing, but a couple of things you could look into:
- Furano is known for it's lavender which should be in season when you're there.
- Asahidake Onsen is a village in a national park with a cable car going part way up a volcano - I imagine it would be a nice place to walk in the summer.

Close to Tokyo, I really liked Kamkura, especially the giant Buddha, and it's easily visitable as a day trip from Tokyo. Nikko also has some beautiful shrines, but it was a ghost town in the evening in February.