I would suggest the White Pass Railroad in Skagway and Juneau for your whale watching; Ketchikan would probably be best for salmon fishing. All can be booked independently on the internet and you need not worry about getting back to the ship in time; believe me, it is in their best interest to get you back--their livelihood depends on it. One name that comes up a lot for whale watching is Capt. Marvin; just Google him.
Hope this helps a little. By the way, Hi neighbor!