The thing about whale watching is that it is a longish ride on a boat, perhaps a distant sighting of a spout, some flukes going under, and then a longish ride back. Honestly I am afraid a 6 y o might find it boring. If you do try it, I would recommend the ship's excursion on Allen Marine, which will give you a big boat where the kid can move around, comfortable clean toilets, and a snack bar. All of this might keep the youngun entertained during the search for whales.
These pictures are from a sea otter trip in Sitka, but actually are the best whale sightings we have ever had ...
And they show the Allen Marine boat and in fact some kids aboard.
In Skagway, IMAO unless you are really big train fans, the best thing for a family to do is to pre reserve a rental car with Avis and drive over the White Pass at your own pace, stopping now and then to admire the scenery and let the kid stretch their legs, and go on to Caribou Crossing in the Yukon for the sled dog cart rides! Everybody of all ages will love this!
Check out our trip report and pictures at Driving from Skagway into the Yukon
In Ketchikan the totems are interesting, but perhaps Saxman Village would be better since it includes a nice native dance show. Also, we love the Ketchikan ducks and I bet the kid would be thrilled when they splash down into the water.
Check out our trip report and pictures at http://www.bully4.us/alaskaZ.html
and Cruising HAL Volendam to Alaska
Actually I have posted a full page of excursions we enjoyed at
Alaska Excursions Guide
so you might check it out. There are soooooo many choices in Alaska.
Have a GREAT cruise!