Some interesting suggestions here:
Any other onsen towns like Kurokawa Onsen?

Personally I like Tokyo itself for onsen.
Tokyo Onsen
Many are completely unique and I do my very best to experience them as much as I can. They provide a tangible link to the city’s past (hard to imagine a more authentic connection with the Edo period) and yet they are fast disappearing from modern society. Whilst still seemingly plentiful, they are disappearing at a dizzying rate (some of my very favourites from my first visits to Tokyo are already long gone), only a fraction are left, and out of those that have survived some of those are changing into something rather different (super sento).