West Yellowstone is nice because it has so many motel rooms, down side is that (for what you get) it's expensive - and crowded.. by Montana standards
Great rivers not too far away, it can be hard to get in/out of the park with crowds.
Other possibles (all small towns):
- Twin Bridges
- Three Forks
All are pretty close to a lot of water. Depends on how many total went. Looking on a map, you can see what I mean
Missoula.. doesn't have as much 'small' water, that I prefer.. but I don't know it that well, but all the amenities are there. At least 2 nice rivers to float, Rock Creek and even Lolo - all within spiting distance