Kintla Campground and Lake are probably the most remote car accessible areas in the park. I think its in part due to the trip up the North Fork road (35+miles) and then the 17 miles in from Polebridge. I made the trip alone in Sept of 07. I soloed with my 17 ft kayak to the back country campsite. Stayed one night, hiked to upper kintla and returned home to Kalispell the next day. It was memorable due to the brillant early fall colors, the big Black bear browsing in a meadow and the incredible solitude. I also experienced the rath of the wind on Kintla in the afternoon. Two foot waves with whitecaps over the bow of my kayak. It was a great ride and lots of fun, but I was happy to get back to quiet end of the lake.
Bowman is also notable for its afternoon winds. I know folks who have abandoned boats and hiked out due to wave conditions. Always be prepared for cold water immersion and wear your PFD on any of the park lakes.
Both Many Glacier and Two Medicine are more accessible for 7 day visits. Don't forget as you drive by Lake McDonald with your canoe that any day paddling on good old Lake McDonald is a good day. If the Sun road isn't open, then Two medicine would be best for camping on the east side of the park. The view in the morning at Two Medicine is hard to beat, anywhere.