Out of Juneau, there is Coastal and TEMSCO. ERA, may not direct book ship passengers due to ship contracts.
In Denali, there are some raft companies, right across the street from the Princess. But, determine WHAT you want. The range, depending where they put in goes from a float to white water tours. Here are listings- http://www.denalichamber.com/
Talkeetna Aero offers flightseeing out of Denali park. Fantastic vendor, I have used several times. Summit flights are my favorite.
The Ketchikan tour, may be ship contracted, but do a search-