If you are thinking about the Alaska Marine Highway System, go to
www.dot.state.ak.us/amhs/pets.shtml. They indicate you can visit the car deck "several" times a day. We have done this but wit cats so that experience doesn't apply to dogs.The ferry system is limited by Coast Guard regulation.
Keep in mind that putting a big rig on the ferry is expensive and then some. You can go from washington to Prince Rupert or to Haines but if you want to cut out the worst part of the road, Haines Jct to Tok, you have to go all the way and that gets really, really expensive.
The best thing to do, unless you just want the coastal experience which is worth a trip by itself, is take your time, drive civilized, unhook the toad in the worst areas, and enjoy. We have made the trip at least 6 times without incident in our motor homes with toad.