We did all our port Adventures through Disney for ease. But two out of our three could easily be booked independently. In Skagway we did a helicopter flight to a glacier and walked about. This was through Temsco helicopter tours, and it is literally right next to the dock. Just walk on over. In Juneau we did Taku Glacier Lodge flight plane tour. It was a flight plane over glaciers out to a remote lodge for lunch and exploring by a glacier. It was with Wingsairways.com Lots of people on our tour were independently booked. In Ketchikan we went out on our own hiking. The only one we could only have booked through Disney was the Tracy Arm boat tour. Then tender up to the Wonder, you climb about a much smaller boat for a close up tour of the glacier. Completely worth booking and can only be done through Disney. My suggestion is to read through the Disney port excursions, find a few that sound good to you, then google the descriptions for them at each port. Most, if not all, run independent tours as well. Lots of cruise ships in these ports in Alaska.
You can read about our experiences for our Port Adventures starting in Skagway here
http://frequentlyaskeddisneyblog.com/disney-cruise-alaska-part-24/