For our 30th anniversary DW and I got off the eastbound Empire Builder in the morning. We were picked up by the van from Meadow Lake resort. After we got checked in we called for the rental car to be delivered to Meadow Lake.
We drove up as far as Lake McDonald Lodge. Our condo at Meadow Lake was much nicer than anything at Lake McDonald Lodge.
The condo had a hot tub.
We were allowed to leave the rental car in the parking lot of the Amtrak station in Whitefish when we left on the Empire Builder for Chicago.
Get started early in the morning from Meadow Lake to head up to Lake McDonald and up over Logan Pass and down to St. Mary.

The park lodges do tend to be more rustic than accommodations outside of the park, but the views from teh lodges are incredible.

Not sure how long your stay in Glacier will be, but if it's more than a few days, I would strongly recommend splitting your stay between the west and east sides of the park. The west side offers other activities like whitewater rafting and horseback riding, but the east side (specifically Many Glacier) is the more scenic part of the park and will offer more opportunities to see wildlife (specifically bears). The Many Glacier hotel has been remodeling, so perhaps you could ask for one of the newer rooms.

As far as shorter hikes, on the west side I would recommend Trail of the Cedars and Avalanche Lake.

http://www.hikinginglacier.com/avalanche-lake.htm

Plan on spending an entire day driving the Going to the Sun Road. The traffic will be slow due to construction, but you'll want to stop along the way for views and short hikes. At Logan Pass Visitor Center, take the hike up to Hidden Lake Overlook, where you're almost always guaranteed to see mountain goats at the overlook.

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

If you enjoy waterfall hikes, stop at St. Mary Falls trailhead and take the hikes to Virginia Falls and St. Mary Falls.

http://www.hikinginglacier.com/virginia-falls.htm

If you do make it over to the Many Glacier area, a lovely, flat hike around Swiftcurrent Lake is a good place to see wildlife, especially moose.

http://www.hikinginglacier.com/swiftcurrent-lake-nature-trail.htm

Whatever you decide, think about making reservations ASAP, especially on the east side of the park.

Enjoy your trip!