Meadow Lake Resort near Columbia Falls is one of the best places my wife and I have ever stayed. http://www.meadowlake.com/
One thing I am quite certain about is that the Going to the Sun road will be closed by snow sometime in late September or early October. You can leave the rental car from the Kalispell airport at the Amtrak lot in Whitefish. I did it and then took the Empire Builder to Spokane. It's your choice if you want to check into the Davenport for the rest of the night in Spokane before renting another car to go to Idaho.
The Empire Builder arrives in SPK sometime between 1-2AM when it runs on time. My last trip it arrived 30 minutes early.

Thanks Tom!

I would go the earlier week just because more of the Park services will be open. Whitefish is my favorite place to stay, but it takes a while to drive to the Park. I like the restaurants and shops in Whitefish. Check out the Garden Wall Inn or the Whitefish Lake Lodge. It isn't going to be as convenient as Columbia Falls, though. It just depends on how much you want to drive. I'd look at Bigfork, Columbia Falls, and Whitefish over Kalispell, though.

You'll definitely want the first week of September as stated above, some park services start to close after Labor Day. Also, if you're wanting to do any ranger-led hikes you'll still have a few options.

Whitefish is about 30 minutes just to the west entrance of the park. If you want to drive the Going to the Sun Road from Whitefish and visit Many Glacier - the most scenic part of teh park - that will easily take all day. If having shops, restaurants, etc., for nighttime enjoyment is the most important part of your trip, then Whitefish. Although, I found after one night of walking around, we'd pretty much seen it all. If you stay in Whitfish, try Bailey's Bed N'Bale. Personally, I would recommend staying in West Glacier or Columbia Falls at Gentry River Ranch or Moss Mountain Inn.

If you're looking to get the most out of Glacier National Park and see the best scenery, then I would recommend staying on the west side of the park for 1-2 days and on the East side of the park for 2-3 days - preferably Many Glacier.

The Many Glacier Hotel has a lovely restaurant, provides entertainment at night and sits right on Swiftcurrent Lake with spectacular views.

Most people don't realize just how spread out Glacier is and how long it takes to get from the west to east side of the park.

http://www.hikinginglacier.com/about-glacier-national-park.htm

For great wildlife viewing, be sure to take the short walk/hike to Hidden Lake Overlook. The trail begins at Logan Pass Visitor's Cetner and part of the trail is on a raised boardwalk. You're almost always guaranteed to see mountain goats at teh overlook.

http://www.hikinginglacier.com/hidden-lake-overlook.htm

Whitefish is a must see town with a Frank Lloyd Wright office building, a crazy art deco railroad station, lots of great bars and a real downtown hardware store, but it is a lousy place to stay if you are serious about doing Glacier.

Macdonald Lake is about an hour away, and that is just the west side of the park, though by no means the entrance.

I'd say the earlier the better. We stayed in a privately owned cabin on Hwy 2 in the tiny community of Essex. I liked the location because you are going to have to drive Hwy 2 to get from East to West Glacier (and vice versa). Staying there means your in the middle, just south of the park (literally). Look at the family owned Glacier Haven inn with cabins and the historic Izaak Walton Inn. There are just a few options of places to eat but the owner of the cabin loves the bar and restaurant of the IW. We ate our big meal in the park and then picked up stuff from dinner at the East Glacier Trading Post. Love that place - they have a little bit of everything including great pizza.

Thanks for all of your great suggestions.

We stayed at the Hampton Inn in Kalispell for one night when we went to GNP and it's a VERY nice hotel. If you can get a really low rate and don't mind the 45 minute drive to the West Glacier park entrance each morning/evening, then I'd certainly consider staying there for 3 or 4 days.

The one place I would NOT recommend is the Many Glacier Hotel. It's got a great location on the east side of the park and the common areas are very nice, but the rooms border on being "dumpy" and there is little-to-no sound insulation between the rooms.

Kalispell has LOTS of hotel rooms, lots of good to excellent restaurants and plenty of shopping if your into that. The 30 to 45 minute drive to West Glacier, the west entrance to the park, is not in heavy traffic but a pleasant drive.

longhorn, we stayed at the Many Glacier Hotel last year after hiking and staying at the Granite Park Chalet. It seemed like our room was recently remodeled. It's an old Park hotel, so the rooms are small, but ours had new flooring and fixtures. I was kind of surprised at how nice it was. I definitely agree that the common areas are beautiful and the view from the deck is amazing!