Does your cruise go to Glacier Bay? You might not need the additional Tracy Arm excursion. My guess is that your cruise line might offer one that works with your times if you really want to do it.
And while I hate to be all doom and gloom, you might want some plan Bs. With no cruises this year, a lot of the providers are really hurting, and the landscape might look a lot different next year.
Really, you can't go wrong with anything you do. When I went a few years ago (I'm really due to go again), in Ketchikan we did a boat tour that we saw Eagles and Totems. In Juneau, we took a bus to/from Mendenhall Glacier and did the visitor center. Considered doing the tram, but it was extremely foggy. In Skagway, we did a train/bus combo up to Carcross. With the exception of Juneau, we did ship tours. I would have enjoyed a whale watching tour, but my wife gets seasick on the smaller boats. Fortunately, she did ok on the boat in Ketchikan. From what I recall, Ketchikan can be walked (Creek Street I believe) and is near the port. Also a small walk from the port in Juneau is the downtown area.
Again, it really all depends on what you want to do. Another thing to consider, after all the touring you are doing precruise, you don't want to end up on the cruise all exhausted. Looking at Glaciers are great (some of my favorite pics are of the blue ice we saw on the way to Dawes Glacier (couldn't get into Tracy Arm). But, unless you happen to catch on calving, at some point, they all start to look alike. If you are going to do the 26 Glaciers tour before even getting on the ship, do you really want to do another glacier excursion?