[odonata]

I am going to have to recommend the onsen theme park at Odaiba. Apart from the touristy shop and entertainment section the onsen itself is awesome.
They have two outside onsen and various inside onsen as well as a sauna and cold plunge pool.

If you want to do onsen and need to practice then the Odaiba onsen is a good place to pick up tips.

To go one better then hire a room with private onsen in places like Hakone.