I would suggest a whale watch trip in Juneau. Also there are busses from the dock to/from Mendenhall glacier if you don't want to take the time for the salmon bake combo tour. Don't miss the glacier in any event. If the weather is good go up the Mt Roberts tramway. No need to prebook this. The tram is right on the dock next to the ships.
I second the White Pass rail recommendation. This is a wonderful trip.
I assume you're stopping in Ketchikan too? Easy town to walk around. Go up the funicular and walk down the married man's trail. The Duck tour is goofy but fun and you get a nice tour of the city and marina area.
We didn't do this but I've heard good things on the lumberjack show.
Glacier Bay is beyond words. Photo's do not do it justice. But take plenty of photos anyway!