I have gone into the backcountry the last couple summers. Last year, we went up to Big Trout Lake and stayed there a couple nights. There are some beautiful campsites on that lake, but it is a bit of a treck to get there. We trolled for Lake trout in the evenings and mornings. I used small silver panther martin spinners with a 3-way swivel with about a 1-ounce wieght at the one end (you can google this method for more information). You have to paddle slow and get down deep to find them, espicially in the summer months. I didnt get into any trout on Tom Thompson, but I did catch some nice smallies around the islands. Burnt island lake is beautiful, but campsites can fill up fast. We always camp at the far end of the lake because I find the fishing to be better there. There is an lsland back there that will be loaded with seagulls. Troll in this vicinty to find the lakers, using the same method. You can also find some nice smallies in the bays and around the rock points.
You could also try jigging for lakers, I have buddy that goes up every spring and does well. But they usually bring a portable fish finder to locate the fish.
Good luck, you will have a great time, I look forward to this trip every year!
Justin Walsh