My suggestion is go to a small family run place rather than an old 70's resort style inn (though those can have their own charm).
If using google for research, look for more Japanese reviews, or if reading tourist reviews, make sure you're looking for the same type of experience as them.
I have found some really nice, small places using
Jalan in conjunction with tourist booking sites (or sometimes use theirs). You can actually get better deals from foreign sites sometimes.
There are some nice new high end places as well. I went to the onsen of one in Hakone when it was brand new about 10ish years ago, and it was very nice.