Most people think the itinerary going from mainland Alaska south (or vice versa) is superior to doing a roundtrip inside passage cruise from Seattle or Vancouver. This means starting or ending at Seward (Anchorage), and also starting (or ending) at Vancouver in most cases.
Of course most of the cruise lines do these itineraries. You might want to look at Holland America or Princess since they do have the best infrastructures in Alaska and have done Alaska cruises longer than the other lines. I believe Princess has one of their small ships there too.
But I will note that the round trip from Seattle we took in 2008 on Splendour Of The Seas with Royal Caribbean was a wonderful cruise. We got about 100 feet or less from the face of a glacier. It was perhaps the most serene morning I've ever experienced.