well, you are right, shin hotaka has many options so sadly i have not been in all ryokans to tell you about all of them
i can just tell you of the very beautiful rotemburos i have seen:
* 新穂高の湯 is nicely framed by rocks almost in the river
https://www.google.com/maps/place/新穂高の湯/@36.2649663,137.562812,104a,51.8y,2.13t/data=!3m1!1e3!4m13!1m7!3m6!1s0x601d4884402b9dbb:0x852127d6a98b7a38!2sNakano-yu!3b1!8m2!3d36.2!4d137.6!3m4!1s0x0:0xb8ebbdfe48eb444f!8m2!3d36.265148!4d137.562638?hl=en-US
* you can go up the ropeway: Shinhotaka Ropeway (i didnt found it so special, since i am from a country with many mountains and ropeways, also i am generally in this area during summer or winter, so i never saw the real koyou, but you seem to be there in the right time, so might give it a try)
* 白出大滝 is secret, super nice, but you need good mountain equipment and i think it is probably a little bit too hard for just casual tourist
https://www.google.com/maps/place/白出大滝/@36.292918,137.6291481,1186m/data=!3m1!1e3!4m13!1m7!3m6!1s0x601d4884402b9dbb:0x852127d6a98b7a38!2sNakano-yu!3b1!8m2!3d36.2!4d137.6!3m4!1s0x601d451469ea2797:0xcaa3449c61ebc1ac!8m2!3d36.2929173!4d137.6291482?hl=en-US
* but: drive to sanbon taki: it is a super easy walk and extremly beautiful
https://www.google.com/maps/place/Sanbondaki+Falls/@36.1311459,137.582...**
https://www.youtube.com/watch?v=HhhSHkR1opI** you can also combine sanbontaki this on the same day with shirahone onsen, Awanoyu, a very famous onsen for blue water where it is even mixed (dont worry, due to the blue color of the water noone is going to see you naked)
https://www.google.com/maps/place/Awanoyu/@36.1459226,137.6244923,319m...*** after you saw Awanoyu, you can go also to the next door facility かつらの湯丸永旅館 which is not so famous as Awanoyu, but therefore more quiet
* Hirayu Onsen with its Hirayunomori is also nice. it is also a good place to stay from value / money
https://www.google.com/maps/place/Hirayunomori/@36.1907264,137.551547,...* when you are in this area, try Hida beef, it is considered one of the best of Japan (take care, it's expensive!)