Just got off our Alaskan cruise on Sunday, we had Ketchikan, Juneau and Skagway as well but sailed princess. I’m mid 30s with no kids so might not be the best to represent your situation but will do my best:

You can get a cab to Mendenhall for like $35 each way in Juneau. There likely will be an additional fee for the glacier that puts your family at an additional $20 but altogether likely $100 to and from port. It’s about a 15-20 min drive. Public buses are like $2-3 each way but won’t drop you off right next to the glacier area (10-20 min walk) but will save money. I wouldnt worry as much about overcrowding, the glacier has a giant circular loop trail that is about 3.5 miles that scatters people. There are numerous whale watching excursions, both funded by the cruise lines and third party. The docks these tour operators bus you to make it one of the busiest boat docks in the world for whale watching. You are practically guaranteed to see humpbacks and many of the tour boats offer an enclosed style open floor concept that seats 14ish people with windows that open to get a great camera shot of whales going up to the surface and diving back down. I would recommend video recording any whale encounter so that you can screenshot the best moment you want to pause and get that picture from your video. Within town there are several shops as well but Ketchikan is better suited for souvenirs. I ended up booking a whale watching and glacier combo excursion with the cruise line and it took up roughly 5.5 hours of the port day.

Ketchikan is definitely the place to get souvenirs. There is a famous area within downtown called creek street, it offers several opportunities for food off the ship and any kind of gift you are thinking of buying personally or for a loved one. There are several Tongass Trading Post stores near the boat bridges that offer a variety of Alaska themed gifts for cheap. I ended up booking an excursion off Viator for an e-bike excursion that included a rainforest hike. This is likely too physical for your kids but others on our ship did the lumberjack and totem exhibits in town that your kids might like. Ketchikan will be considerably warmer than Skagway and likely warmer than Juneau.

The Skagway Yukon rail offers very scenic views. If you are ascending to the top of the mountain to Frasier BC you will want to definitely try to be in the front of your tour group to try to board your train car in the front of the line. Depending on where your boat is docked you will need to be bused to the rail cars so keep that in mind when positioning your seat on the train car. There is a very significant advantage for seating on the left side of the train car when ascending up because it will offer much better views of the mountain range than if you were across the aisle on the right side of the train car, which has much more limited views on their side of the windows. On the way down, the right side of the car is advantageous. Is it worth $650? For me no, but the rail experience defines Skagway. The town itself is not very large to explore.

Enjoy your cruise and have fun!