Are you planning to book with Disney or on your own? Any children (and ages)?
Whale watching in Juneau is great. We've gone twice with Orca Enterprises. We've also done the Pilot's Choice double glacier landing with Temsco Helicopters.
In Ketchikan we've gone twice with Island Wings - once to Anan Creek (for bears) and once to Misty Fjords. Also spent time walking around town.
Once in Skagway we did the dog sledding with Temsco Helicopters. Another time we rented a car and drove to Emerald Lake, making stops along the way. (Used Murray's Guide.)
Alaska is spectacular. If you can, get up in the air (helicopter, sea plane) to really appreciate the size and beauty. Enjoy!