Bladerunner,
I'm glad you asked that question! I was just thinking about that earlier this year, when I went with my non-swimming family to Yellowstone area town, Big Sky. I'd been to Yellowstone the previous year and wondered if there was any water warm enough to swim in during the late summer months.
I'd taken a couple of areas to interest and also did a little bit of research for you, too.
My initial plot for a dive area was Hebgen Lake, part of the lower Madison River. A man-made lake, with the help of the Hebgen Dam, it looks to be rather clear, with dark blue water. I've seen people water-skiing there, so you might want to bring a dive buoy for the ski boats to dodge. It's really pretty and wouldn't mind just sitting on the shore taking in the scenery. Well, I say that now, but it's never long till I'm in the water. You might also want to bring a 5 mm suit, as the water tends to be quite nipply, and no, I didn't mean nippy.
Just on the other side of the dam, and the actual reason, or partial reason for the dam, is Earthquake Lake. I'd love to tell you the history behind it, but a reply posting just isn't the right place or way to tell you, so here's a link:
http://www.billingsgazette.com/magazine/990815_mag01.html
and just to see if you have more luck with info...
Earthquake Lake Visitor Center
P. O. Box 520, Highway 191
West Yellowstone, MT 59758
Phone: 406-682-7620
Let me tell you, it's a pretty eerie place. Trees that once stood tall amongst the river bed, now stand like ghosts, barely above the waterline. Cabins stand in random places, after floating around before the water subsided some after they built the spillway. It might be a good place to dive for 1959 Airstream Trailer underwater booty!
I've really been interested diving there, but you'd have to call the visitor's center there. The nice lady in the brown uniform wasn't quite sure, but estimated that Earthquake Lake was probably 150 ft deep, or so. She might have just said that to get me the hell out of her face. I do tend to have a 3rd grader-like fascination about that stuff. I'm still not sure if you can dive there. You might need special permission. Again, I dunno.
Flathead Lake, from what I gathered, has camping, fishing, and swimming facilities. It is 27 miles long, 15.5 miles wide and 370 ft. deep with 5 cubic miles of water. I haven't heard of any freediving there, much less scuba......even less anyone who has been there. It might be nice, and it might not be. You'll have to check it out for yourself. I'm just throwing these out, here. It'd be cool to say you're the first person who's freedived(dove?) there.
There's another lake called Lake Mary Ronan. I've tried to get the stats about it, but I couldn't find any immediately. It also has camping and swimming facilities.
There are a bunch of beautiful rivers, such as the Yellowstone, and Madison that are fun to swim in, if you can have fun without diving. There's one spot right down the road from Big Sky that me and my older sister like to jump from the bridge with the locals...Just watch out for rocks, I damn near sprained my ankle on one. Let me tell you it's hard to fight off hypothermia, fight a current with one foot, and use profanities all at the same time.
I hope I helped a bit. I didn't even ask you where in Montana you were going to be staying. If you haven't already, go see Yellowstone Park...for the people-watching if not for illegally feeding the cutest, Frito-addicted chipmunks this side of the Earth.
Good luck!