I agree with Harry; I think I was on the next ferry after him--Lots of space on deck, and a nice respite frim the Dempster. We took the ferry from Skagway to Prince Rupert, cost about $600 (Canadian) for the bike, me and a room. I like the room even if it's just a secure place to stash your stuff. The stops along the panhandle are worth seeing, but very short, and often at weird times. It also seems to me that if you get off there, you have to get back on there, as the only road into a panhandle town is via stewart bc- the rest are local roads.
The boat staff were quite helpful to us; the onshore people were bureaucrats in every sense of the word. I did all reservations by internet.