Just returned from a fantastic Alaska cruise on the Coral Princess.
In Skagway we rented a van (with another couple) and drove into the Yukon, as far as Emerald Lake. We rented our van from PB Cruisers, which I would not recommend -- go with Avis instead if you can still get a reservation. You will drive through much of the same area as the train, but will have the advantage of stopping when you want, etc. Easy drive -- can't get lost.
In Juneau we opted for a tour with Orca Enterprises, Capt. Larry. Excellent. We had pre-arranged for the van driver to take us over to Mendenhall Glacier and she wait while we walked around. We didn't have a lot of time in Juneau, so we weren't able to stay very long at Mendenhall.
In Ketchikan, we booked Island Air Wings for a seaplane trip into Misty Fjords. Gorgeous. Afterwards we lunched on Burger Queen (best fish & chips I've ever eaten) food while having a beer on the back deck at Artic Bar (across the street). Afterwards, we had a Highlights of Ketchikan Tour from Sourdough Tours. We went to Totem Bight AND Saxman Village, as well as a drive through the town.
You'll have a great time