I've not been to any of the above places you mention. I just had a quick look at these places.
Beniya Mukayuu is in Yamashiro Onsen, Kayoutei in Yamanaka Onsen, the other two in Takayama.

Takayama imo is not exactly an onsen mecca. There're some hotels there with onsen, but the real onsens are higher up in the nearby mountains (eg, Hirayu, Fukuchi, OkuHotaka) or down the valley in Gero. Maybe these ryokans are good for the ryokan experience, but I'm not sure that the onsen experience would match up to a lot of other places.

Beniya Mukayuu does not have the best onsen characteristics according to the guidebook I use to judge onsens. Kayoutei seems the best of the bunch, but it seems it's hard to get to from the nearest train station.

I've not been to Yamanaka Onsen. Maybe it's great. Kayoutei looks good, but again I've not been. Awara Onsen and Katayamazu Onsen are two of the other onsen towns in that general area, and they seem to have seen their better days.

As far as I'm concerned, the room at Yudanaka's Aburaya Tosen with private en-suite onsen is plenty high-end. The quality of onsen water there is definitely a notch above that of Katayamazu or Awara Onsen, although I can't comment on Yamanaka Onsen.