If you're looking for whitewater, John Steven's Canyon just above W. Glacier is probably your best bet. I believe the upstream access is typically made at Moccasin Creek.
I also am heading up to the Flathead this weekend and am looking for some good rafting. I'll probably try and do about 20 mi. on the MF of the Flathead. Checked flows and they look as if they're screaming, so not too sure what to expect.
I was over on the Lochsa about 1 mo. ago and it was amazing, huge water on a sunny day. One of my best trips thus far.