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If you go to Glacier National Park, make sure you stop at "Many Glacier". There is a boat ride on Swift Current Lake that takes you to place where you do a ranger guided hiking tour. You may even run into a bear like I did.
Agree about Waterton, Prince of Wales Hotel is great, fantastic view of the lake, recommend going on the tour boat. Really nice trail at Cameron Lake up to Summit Lake on US-Canada border.
Going to the Sun hwy is a must, jaw dropping scenery.
I did both Yellowstone and Glacier on same trip once, I stopped at Butte (half way) and headed up via Missoula, beautiful Flathead Lake and stayed at West Glacier.