I had the same issue a few years ago when my wife and I took an Alaskan cruise. I posted looking for insights about riding trails while in Alaska, but no one was able to help. I cut my losses and just enjoyed Alaska. Ketchikan was my favorite stop on the cruise. It is a beautiful area. We ended up going on a bear watching tour, sampling the local food (ALOT), and checking out the local Klinkit artwork.
If you are into hiking and you are making a stop in Skagway check out the Chilcoot trail. It is a little way out of town and you’d have to hitch a ride, but the views are worth it.
As for biking, I don’t know if you are leaving from Washington or Vancouver. If your port is Vancouver spend a day there and rent a bike. Stanley Park has many miles of trails (some paved), and you are not far from Whistler.
Have a great trip!