I have the same doubts you have about shore tours in Alaska. I´m counting the days to get on board of the Radiance of the Seas with my wife for a cruise around those amazing places in Alaska. I hope we can get some useful answers.
I have only cruised to Alaska on Holland America, but suggest that you won't go wrong in price or quality with the following:
Juneau: 1. There's a wildlife boat cruise that looks for eagles, seals, sea lions and whales [humpbacks and orcas]. It is exceptionally well run, covers beautiful territory and almost guarantees whales. Sometimes combines with a stop at Mendenhall Glacier - also worth while. 2. If you can afford the helicopter flight that lands on the glacier, this is a fun thing to do once; also available at Skagway. Not a "must" unless you don't mind paying the cost.
Skagway: 1. Take the White Pass & Yukon train trip. You will not regret.
Ketchikan: 1. the Saxman Village tour is informative, fun, and different - you could visit here on your own, but would miss a fine show. 2. It is fun to just wander about Ketchikan - if you wish to buy things to take home, try the Eagle Arts shop on Creek Street.
Sitka: 1. I'm told the raptor centre tour is very good. 2. The boat tour that takes you to the sea otters is excellent; whales are a frequent "bonus." 3. Sitka is also enjoyable to walk through.
When you get off the ship in Juneau, there is a building filled with tour operators. You can easily book any excursions that you want there. One very expensive, but great tour, that can be booked in several ports is the helicopter trip to a glacier. I highly recommend this trip.
As someone else has written, the White Pass Railroad in Skagway is great. It's warm and dry on the train, unlike other things in Alaska.
We took a bald eagle trip on the Chilkat river that was great, but cold and wet.
Don't waste your time on an excursion called Orca Beach Hike in Ketchikan.
We did not go on a whale watching trip because we expected to get to see whales from the ship. We did, but the distance factor made them almost impossible to see. Take a whale watching tour. The people that did that raved about experience.