I do see an awful lot of tour buses up in that area, so it can be done. I've never been up there by bus, so it's hard for me to shoot down the idea. But I would still imagine that Oku-Karuizawa area is best enjoyed by driving around at your own pace and stopping by different places on a whim. And that waterfall is no big deal. If you do stop by Karuizawa, I think you should just check out the old town area I mentioned above.

Another option is Matsumoto... the castle there is famous and is one of the few original castles in Jpn.

I just looked up some schedules for you for the Alpen route option and Takayama option. It'll be a long day either way, but it can be done. See what you think.

ALPEN ROUTE:
Shinjuku 7.30a --Azusa express train--> Shinano Omachi 11.02a
Shinano Omachi 11.15a --bus--> Kurobe Dam 12.46p
sightsee ~40min around Kurobe Dam
Kurobeko 13.40p --cablecar/ropeway/bus--> Murodo 14.25p
sightsee ~70min around Murodo
Murodo 15.40p --bus--> Tateyama Station 16.47p
Tateyama Station 17.22p --train/shinkansen--> Kanazawa 19.38p (includes 50min in Toyama)

TAKAYAMA:
Tokyo 7.33am --shinkansen--> 12.14pm Takayama
sightsee ~4hr+ in Takayama (main touristy area is ~15min walk from station)
Takayama 17.16pm --train/shinkansen--> 19.38p Kanazawa