I'd recommend both a flight seeing tour for nice aerials of the area as well as a kayak tour and/or power boat tour for more intimate, sea level views. Kayaking, while a beautiful adventure (given the right weather), can be arduous and time consuming while a tour boat will provide easy, fast access to the glaciers and various photogenic spots.
I have experience renting kayaks from these folks and can recommend them:http://www.glacierbayseakayaks.com/
Here are a couple good general resources:http://gustavus.com/activities/http://www.nps.gov/glba/planyourvisit/index.htm
While in Gustavus, I'd also recommend a whale watching tour to Point Adolphus either by kayak or power boat.
Cheers and have fun!