We've taken the Prince Rupert to Haines run many times in both directions and have always enjoyed the time off the bike. But always ready to be back on the bike after a couple days on the ship. If I wanted to be on the west coast in a hurry the ferry would not be my choice. Riding the Alcan is, or certainly could be, less time. For most of us the best combo/compromise in time and money is ride to Haines and ferry to Prince Rupert since the Gulf Cross and YPR to Bellingham segments add significant amounts of both. I find the AMHS online reservations system gets what I want but the phone support is good too. If you've never taken the ferry, do it at least once.
I've never heard of getting passage on the freight ships but that would be interesting to try. Anyone ever done that?