I went last year but did not go with Disney. We used Beyond Skagway to go into the Yukon from Skagway, and they were great. They customized our trip to what we wanted to do. (I know they offer a treasure hunt for families.) Personally, I would not do the train. I did the road both ways, and it was great, because we could get out and stretch and move around. We even got to drink some fresh water from a mountain waterfall (which is not an everyday occurrence in the part of Texas I'm from).
The trip was a long one, but it never felt long. We went to the suspension bridge but did not cross it, and there is also a summer dog sled camp in Tutshi (pronounced too-shy) where you can stop.
If you like pictures, the Yukon is a must do...there are so many different types of landscapes. It's just beautiful!
I used to teach kids the age of yours, and I know how they can be, so I'd probably rent a car or take a private tour. Skagway is very small and touristy (great for shopping but not a place to keep most 12 and 14 year olds interested for long), so it's definitely best to get out of town and see the scenery.