Sounds like a fun trip. We have been to Yellowstone and just went to Glacier this year. I would be concerned about the time of year. You might not be able to get in to much of Yellowstone and Glacier had only 15 miles of road open this year until June I believe. Based on where you are going and coming from, the east side of glacier is where you want to stay. It was closed this year so I can't say much. Definitely a place to get out and hike, plan on hiking up hill as it is just a mountain and all the trails are long and up hill...
In Yellowstone we stayed at Fishing Bridge. Not great, but not bad. But, a good location since most of the park is a drive between places to view. One year we had snow on the 4th of July when there. So, you never know. I would start booking camp spots as soon as they let you. It fills up fast. Same with Glacier.