Don't go to Juneau without heading out to Mendenhall Glacier. (We actually rented a car since we have been there so many times. There is now car rental at the cruise ship dock.) Black Bears are almost an assured sight if you stay at the Glacier long enough. Also, the whale watching expedition is the best anywhere. Don't pre-order the Mount Roberts Tramway. If there are low clouds, it is basically a waste; but if you can see, it's well worth it.
Skagway has a lot more options for fun than one might think. First-timers should sure take the train. Dyea is a hidden gem if you want to get out of town. Taking the fast ferry to Haynes may just give you a chance to see bald eagles and brown bears if you can get over to the Chilkoot River. The town itself has a lot of charm.