Hara Museum of Contemporary Art in Gunma
You can find nature in Japan! And you may find it about 1hour and a half away from Tokyo: in Gunma prefecture.
There is that contemporary art museum in the middle of the mountain that is fabulous. It is managed by the Hara Museum, and hosts collections that do not fit in the mother museum based in Shinagawa (a wonderful place to visit, as the house is build in a colonial style and hosts quite surprising art. Is this really art? is one of the question you may ponder,sipping a glass of wine in the garden of the museum - especially lovely in spring and autumn)
In Gunma, there is a lot of space. There are even sheep grazing around. The art is, well, contemporary, and staged in a huge wood building as worth the visit as the collection.
There is a coffee shop there too. They serve a very good cafe latte and you can enjoy Andy Warhold art sitting in a chair designed by Eric Starck.
If you have time, you can go to some public hot spring in the neighborhood and relax.