I've not been to Hubbard Glacier. I've heard it is even more impressive than Glacier Bay.I think you will have a great time.
We took the Skagway train a few years ago and were not impressed. It is cute but very slow. The scenery is very Washington and Oregon like and not spectacular to we norwesterners. The "Liarsville" mining camp is pretty bad too unless you are a seven year old kid. You may just want to go off and do your own thing there. I bet you could rent a car for a reasonable price and just go exploring.
I'm jealous, have fun!