Can't help with cruise advice, having never been on one, but can recommend things to do on shore excusions!
If you have a hankering to fly, I would recommend a flight-seeing tour of the Misty Fjords National Monument if you arrive in Ketchikan with decent weather. It's truly breathtaking from the air, and there's really no other way to see it in a day. Several air tours will land on one of several lakes, or on salt water, to give you a different perspective of the area, but it's pretty spectacular.
If you still want to fly, there are several helicopter tour companies in Juneau that will take you up on the Juneau icefield, where you can hike on the glaciers, go on dogsledding tours, climb ice cliffs, or just take in the sights. There are also floatplane trips out to the Taku Glacier Lodge for a salmon bake or just to do flight-seeing over several glaciers. If you don't want to fly, take a tour out to the Mendenhall Glacier and hike out to Nugget Falls or hike the East Glacier trail.
In Skagway the thing to do is the White Pass & Yukon Route narrow gauge railroad. It is simply outstanding.
Hope you enjoy the visit, Alaska is fantastic!
Chris
