I agree with others to hit the Bison Range on the drive up from Missoula. The kids will get a kick out of seeing bison, antelope and elk from the car.
If you really want to hit Glacier hard, you are going to have long days driving in from Whitefish every day. As others have mentioned, Avalanche Lake from the west side and Hidden Lake from Logans Pass are two of the easier, more scenic hikes in the park that are great for kids. For this reason, they are also the most crowded so get there early.
I prefer the east side of the park to the west side. Many Glacier and Two Medicine are neat areas with lots of great hikes. Most hikes are probably farther than your kids will want to do. If they are up for some longer distance though, Check out Cracker Lake or Iceberg Lake. Bring bear spray.
Take hwy 83 through the Swan on your way back to Missoula. Holland, Rainy, Alva, Seeley and Placid are all neat lakes to check out.
I wouldn't be too quick to decide which river you want to fish. Book a guide, and let them decide what river is fishing the best based on current conditions. They fish the area every day. The Blackfoot, Clark Fork, and Bitterroot are all good, but can vary based on water levels, temperature and hatches. Rock Creek is tons of fun, but no floating is allowed after June so your guide will most likely steer you towards a river that he can row you down. If you can ever swing a separate trip dedicated towards fishing, book a guide on Rock Creek first week of June during the salmonfly hatch. Blackfoot River Outfitters, Grizzly Hackle, Kingfisher and Missoulian Angler are all great fly shops to book through.
Missoula will be good for breweries and food. Notorious P.I.G. bbq and Big Dipper ice cream are what I would hit first. Tamarack Brewing or the Top Hat for good burger/pub food. Lolo Creek Steakhouse if you want to splurge for a nice steak. It has lots of cool animal mounts on the walls for you and the kids to check out. Kettlehouse, Draught Works, Great Burn, Missoula Brewing, Bayern... all good breweries to hang out and tell lies about your fishing trip. If you like dark beer, try Cold Smoke scotch ale by Kettlehouse. You'll thank me later.