Skagway: Booking through Disney, we did the White Pass railway to the Canadian Border (very pretty), bus back (meh) to Yukon Gold Rush dredge and panning experience (tourist trap!) and walked around the town a bit for some shopping and had lunch in town.
Juneau: booked independently through Alaska Galore tours and did the Whales, Bears and Glaciers tour. It was awesome and the highlight of the entire trip. Highly highly recommended. We were the first off the ship and were back an hour before departure time. Had a personal tour guide with us all day. First went in small plane to Chicagof Island to meet a native tour guide and go see bears. DisneyNature had just wrapped up filming "Bears" and we recognized a couple of sites. Back in plane to fly over 5 glaciers, narrated by pilot with headphones. She really got down in some valleys then swooped up and over. It was literally awesome! Then went on small boat for whale watching. About 12 people total. Up close and personal. Lots of humpbacks putting on a show. Felt sorry for folks on the large boats. Some dolphins raced the boat back across the bay. It was a lot of fun.
Ketchikan: walked around in the morning, up Creek St to the salmon ladder, took the funicular to the lodge, saw Totem center and hatchery. Booked independently with Southeast Sea Kayaks. Met guide at the visitor center and walked to pier. They took us to Orca Cove where we met our kayaking guide who took us (family of 4) on a 2 hour paddle. Saw sea stars and eagles but no orcas. It was quiet and beautiful, very peaceful. Delicious smoked salmon lunch afterwards. Back to ship in plenty of time. They knew the ship schedules better than we did, so no worries.
Don't worry about booking independently of Disney. I felt we had better, more personalized service, much smaller group, well, it was just us most of the time, and we were well taken care of. It was nice to meet locals, not just summer hires for the cruise line.