You can catch the Bellingham to Ketchikan ferry, probably have a couple-day layover, then catch the Ketchikan to Homer ferry.
But the Ketchikan to Homer route only runs from June through September.
If you're going sometime soon, I would say your best bet would be to ship your guns to a dealer at your destination city. I drove the ALCAN last summer, from Homer to Fairbanks, to Edmonton, to Michigan. Not a single problem on the way. There weren't any "shady" spots that I saw enroute. The "shadiest" place I stopped was a 1-pump gas station in the middle of the Yukon ran by a very nice (although chatty) elderly lady.
Why are you going up there? Is it for a hunting or fishing trip? Moving via PCS (which would mean you're either USCG or USAF). Just going up for a vacation?
I can tell you a dozen different ways to get your gun to your destination, including getting it (legally) through Canada. I just need to know where you're going and why. I spent 4 years in AK, should be going back for another 4 years next summer. I'm pretty familiar with the laws and ferry routes. Let me know, I'll offer whatever help I can.
"To preserve liberty, it is essential that the whole body of the people always possess arms, and be taught alike, especially when young, how to use them." -Richard Henry Lee, Virginia delegate to the Continental Congress, initiator of the Declaration of Independence, and member of the first Senate, which passed the Bill of Rights.