There are a number of
very high end Ryokan in the Japanese Alps, that would qualify as ultra deluxe by everybody, even Wallpaper*. The winter issue of
Kateigaho has an very nice article about their favorite onsen ryokan. There is also a book called
The Japanese Spa, which has some pretty nice ones too. You can also try the
Luxury Ryokan website.
Lastly, if Western is what you are looking for, my favorite is definitely the Imperial Hotel in Kamikochi. Not "luxury", since it is hard to do this well on a 70 year old building that is inaccessible 9 months of the year, but it is a wonderful experience. In keeping with Japanese inscrutability, there is no mention of this property in their English website. You have to go to the Japanese side to actually realize it exists
here. Although they will be surprised that a foreigner has found out their little secret when you call up for reservations, they'll gladly take your money.