I'm taking my 3 & 7 year old to Alaska in May and hard a very hard time finding fun excursions everyone could do. If you want to kayak, I would suggest renting one through a park service or independent company in one of the ports. In Sitka, we are renting a car to do some hikes, there are a few companies there that rent kayaks in addition to their guided kayak tours which your 4 year old probably won't be old enough to go on.
In Skagway we are doing a flightseeing tour to Glacier Bay with a beach landing. I also looked into the helicopter & dog sledding tour there which will take 3 year olds. I would also suggest booking a private boat charter in one of the stops. Both Sitka & Juneau had several options. You can customize the tour to include stops on a beach to explore tidal pools and view marine life on the boat. I found several boat captains (2 were even teachers so experienced with children) that would do this on Sitka.
Basically, the cruise ship tours are going to be limited to big group tours that my family isn't interested in but if you do it on your own, you have tons of options.