HAL has itineraries that go to Glacier Bay and provide access to Skagway, with the railway. Skagway port had a rock slide last summer so is a little different currently, but they do intend to take ships this summer (there are multiple threads if you want to read up on it). Most people would recommend leaving out of Vancouver as the inside passage is more scenic (we chose Seattle because the flights to Vancouver were much more expensive for us).
What kind of wildlife are you looking for? Many of the ports have good whale watching. We opted for a kayaking tour in Orca Cove out of Ketchikan which may provide wildlife viewing. Our cruise doesn't go to Skagway so we aren't doing the rail tour. Another option is that some cruise lines, for the Juneau port stop, offer a small boat excursion up Tracy Arm Fjord to see the glaciers up close, and I've also heard it frequently has good wildlife viewing, including possibly whales, eagles, and otters, and maybe seals. There are some recent threads on that tour as well, and it comes very highly recommended even though it's 7 hours on a small boat.