The cruise ship excursions seem pretty expensive. Can anyone suggest specific local tour operators? Specifically, we're interested in history, wildlife, and calving glaciers. Thanks!

I forgot to say that this is for an inside passage cruise on HAL this August.

You need to determine WHAT tour you are looking at- THEN find a local vender. Plenty available, but they are specific for the activity. I never use middle men in Alaska either. You should see glaciers from your cruise ship, WHAT type of wildlife??? This are is mostly marine with Juneau whale watching superb, consider Orca Enterprises. History is Skagway- free are Park Service activities http://www.nps.gov/klgo/schedule.htm
But tops is the White Pass RR. Tours in Alaska are costly no matter how you book them, they are also well worth the costs so consider budgeting fully, you get only half a trip without them.

What are the thoughts on the White Pass RR trip vs the bus trip? Which is a better experience?

If you have an interest in history, then definately the train, superior for scenery as well. There are combo trips to consider with the train/Yukon trip very worthwhile, the shorter tour is only a return bus from White Pass down the Klondike Highway with a usual stop at Liarsville, a recreated gold camp. A better option in my opinion than a bus is to rent a car, only major is Avis and print out Murray's excellent Klondike Highway guide www.explorenorth.com