I been to Nagano, Hakone, and Hokkaido for onsen and each of them have their charms. What I'm about to say is purely personal opinion:

1. Nagano itself doesn't have much to see, I strictly went there to enjoy the ryokan experience and look at some snow monkeys. It's relatively easy to get there from NRT by bullet train and I rented a car from Nagano to reach the mountain area where the onsen are.
2. Hakone has a good amount of stuff to see but the cable cars can be packed! From Hakone, you can drive to Mt Fuji using car rental in Hakone. I should of get at least 1 or 2 nights in the Mt Fuji area so I can explore the area a bit more.
3. Hokkaido, specifically, Toya and Noboribetsu, are nice but would be better if you have access to a car. Last time I only used rail and couldn't check out the surrounding area because I have no idea about how to use the bus.

My sister went to Fukuoka and seem to like it but it's one of those $500 USD per person per night ryokan. I'm basically going through the list on Japan Guide and see which one peaks my interest.
https://www.japan-guide.com/e/e2292.html