Did the Alaska cruise including those ports a number of years ago on Celebrity. In each city (except Ketchikan) we booked tours independent of the ship excursions for significantly less than ship excursion doing the very same thing. This May we are doing the Alaska cruise on HAL and will be in all 3 ports again and have again booked independent of ship. The tour operators are largely geared towards cruise ship passengers, they track the schedules and most offer full refund if the ship does not make port or is significantly delayed. They will also adjust start time dependent on arrival of ship.
Juneau is well known for whale watching but as we were in Icy Straight Point last cruise that is where we did our whale watching the first time. This time we will do Mendenhall Glacier and Whale Watching combo in Juneau with a local operator.
Skagway is very small so it is good to do a tour here. We previously did the White Pass and Yukon Rail combo with mini van tour to Emerald Lake and back to Skagway. This was a great trip and so we are doing it again.
Last time we did a bear watching trip out of Ketchikan to Traitor's Cove by seaplane (booked through Celebrity). It was a great experience. This time we will wander town and some of the trails, probably the funicular etc.
This forum has a number of private tour operators listed and they have websites. The ones that I have contacted have been very quick to respond to email and are very invested in making sure passengers are picked up when the ship arrives, have a great tour and are back at the ship well in time for embarking. This is their livelihood so they do not want to get a bad rep.