We are also planning to spend time in Yellowstone this summer. We were in Canyon and Madison and Mammoth many years ago and enjoyed all three. I believe Mammoth is first come first served but I know you need reservations for Madison and I think Canyon too, but I'm not sure. Madison and Canyon are more centrally located. Mammoth is close to the Boiling River (hot springs) and we thought it was very scenic, with the wildlife coming through the campground.
A friend recently mentioned that they stayed in Slough Creek and Pebble Creek campgrounds, which are one of the last ones to fill up -- they had no problem getting in (first come) in the morning -- although I'd advise getting there really early. These two are in the eastern part of the park -- lots of wildlife viewing and less crowded but further from the geysers
In Glacier we were briefly in ST. Mary's -- that is convenient, but the part of the campground we would have preferred -- by the river -- was flooded out -- we got to Many Glacier (where you've already been) and stayed there a about a week. It's hard to get into but worth the effort.
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