I've done White Pass Railway both up and down the mountain, and loved it. Some in our group did an excursion where you take the train up, and then bicycle down. I would imagine that is more weather-sensitive than taking the train in both directions. Don't miss the little museum of the gold rush they have in Skagway.
Also, I did whale watching (and salmon spawning watching) in Juneau, while others' flightseeing excursion was canceled due to weather.
You really have nothing to lose by booking in advance. Most ships let you cancel with some advance notice, and as was mentioned, if they cancel the excursion due to weather, you can choose something else or get your money back. Some of these excursions do fill up.