Re: Skagway, consider renting a car and driving the highway from Skagway to Carcross in the Canadian Yukon. No doubt that the train ride is great but I suggest renting a car as a lower cost alternative.
Have a great cruise...you will love Alaska! We found that Juneau was the best port and unfortunately did not have a whole lot of time there. We took an early morning whale watch and it was great! My advice...go with a SMALL boat tour, I believe we had 20 people on ours. The captain of the little boat told us that the humpbacks have learned to stay away from big ships because they are getting killed due to so many ships going through Alaska now. We didn't see a single whale from our Princess ship, and Alaska is loaded with them during the summer months as they migrate from Hawaii. Remember...GO LITTLE BOAT!
We also took a hydroplane ride to an island off of Juneau where the brown bears are. It is a spectular thing to do on a cool day, unfortunately it was 90 degrees that day and the bears would not come out. They usually land the plane next to a beach area where all of the bears congregate. We saw one from above and that is all. I wish that we had gone to the glacier....heard it is incredible! Good luck!
We booked thru Princess, a flight seeing glacier tour. It was absolutely beautiful. No landing on the glaciers though. It was in a small plane (carried 6 passengers)....had a small group. They have larger planes for up to 20 passengers. I highly recommend this excursion. We did this in the early morning.
In the afternoon, we did the Whale Watching Quest and Mendenhall Glacier. We were on a catamaran named Captain Nicholas. It was great! We saw lots of whales and sealions.
Try to book privately with Harv and Marv's Alaska Outback. You will find them on line. They are great great great. Two nice boats for small groups no more than 6 people and fantastic on-time and fun service.
We took the helicopter flight (ERA )that flew over 4 glaciers, Juneau Ice field and landed on one of them. Wonderful experience, especially for DW who had never been on a chopper before. (She is still smiling! )