Best hot spring in Japan

Well, the most famous ones that I know of are Hakone (near Tokyo), Beppu, Yufuin, Kusatsu, Ibusuki. Kusatsu is not hard to go to from Tokyo, so if you're looking for places near Tokyo, then Hakone or Kusatsu would be best I think. Beppu, Yufuin, and Ibusuki are all in the Kyushu area which is the large island at the bottom of the main island.

There are other onsens listed here as well. http://travelience.com/blog/top-10-recommended-onsen-hot-springs-to-visit-in-japan/