They are certainly no secret, but Bowman and Kintla lakes in the northwest corner of the park are both great places to camp and have some fish. Glacier Park is really not spectacular fishing for the most part, though you can get into some good fishing in teh backcountry lakes - like most places the farther you hike, the better the fishing.
It would be wise to take your can of bear spray also. I had to use it in Glacier late last month and certainly would not recommend hiking there without it.
Its a beautiful park, fish or no fish you'll enjoy it.