The AK Ferry (Alaska Marine Highway System) is subsidized and you won't likely find a better price, although you will probably find much more convenient shipping.
AML/Lynden Transport is probably your most convenient, but will cost more.
However, I have started moving boats around by putting them up for bid on uship.com. I was pretty wary of this at first, but we have gotten stellar service from everyone who has delivered anything for us, and the costs have been about 20% of the shipping quotes we've gotten. That's not 20% less, that 20% of.
We had a 25' Safe Boat delivered from New Jersey to Seattle (granted, that's not AK, but it's just a recent example), and got a bunch of shipping quotes all in the neighborhood of $10k. We put it up for bid on uship and got it delivered within a few days for about $1200. I'm sure results vary, but so far, we've been very happy with uship and I wouldn't go paying full price until you've at least given uship a shot.