I can't recommend a particular company as we bring our own boats when boating. However, I can say that Glacier Raft company was real helpful to us last year, in answering questions about logistics, when we did a fly-in trip on the wilderness section of Middle Fk Flathead. So, I guess based on that, I would recommend them. Whomever you may choose, check to see that their style of trips is what you are looking for. Some folks like the scenic floats, others like water fights and lots of yelling, and still others like more family oriented trips. Find a company offering the style of trip that you prefer. Lastly, don't use a company that seems lax in safety precautions. If they don't mandate the use of PFD's (life jackets), go somewhere else.
We did one several years ago. It went along the same stretches of the river that portions of the movie River Wild with Meryl Streep was filmed (scene where her husband sets up the trap to rescue them). The trip was relatively mild (late June/early July) and only a couple of "rapids" mostly easy float. Many warnings about falling in due to extreme cold temperature of river.
We have taken a couple of other raft trips, our best so far has been the New River in W. Va. We also taken the Colorado near Moab, a longer trip and a few more rapids, but still relatively calm (was initially worried with all the dire warnings the outfitters kept making - "people have just died here!" but never experienced anything of highrisk).
FOr the Montana trip I cannot recall who we used as the rafting outfitter, but they were out of the west side of the park.