Juneau - Whale Watch & Mendenhall Glacier Combo with Juneau Whale Watch. They do the whale watch first before going to the Glacier and give you flexible time to stay at the Glacier as long as you choose, with buses returning every 30 minutes. This gives you time to do the hike to nugget Falls or other hikes at the glacier. Just make sure you know when the last bus leaves and allow at least an hour to catch the bus and get back to your ship prior to the all aboard time.
Haines - Rent a car and go to the Kroschel Wildlife Center, have lunch at 33 Mile Road House on the Haines Hwy, go to Chilkoot Lake and Chilkat State Parks for a good chance to see bears, moose and eagles.
Ketchikan - Either the Deadliest Catch tour or a kayak tour with Southeast Kayaks. Ketchikan is easily walkable. If you have additional time, pick up a walking tour map at the visitor center and see Creek Street, Married Man’s Trail, the Fish Ladder and more.