We stayed at both St Marys (no hook-ups - inside) and Johnson's (full hookups just outside the park) on the East side of the park. I prefer the East side because of the scenery on that side of the park. The west side is nice too but it is more heavily treed and more similar to other places we have been. More of the hikes we wanted to do were on the east side of the park so it cut down on our driving to stay on the East Side.
It depends upon whether you are at Glacier primarily to see the park or to spend time in the campground. Johnson's is nice enough but probably doesn't compare to the KOA if you are planning on spending a lot of time at the campground itself versus exploring the National Park.