You'll get answers all over the place on "the top three", since this is so subjective. In Skagway I'd say the White Pass railroad trip. In Juneau one of the dogsled tours on Mendenhall Glacier. In Icy Point kayaking or fishing. In Ketchikan one of the zipline tours.
We have an Alaska tour expert here - CanCanCase is the user name. Hopefully he will weigh in with some good advice.