I assume you have read this page
AMH VehiclesI was shocked when we visited Juneau on a cruise and saw all the 5ers and TT lined up to take the ferry.
I don't know how the individual ship handles them - but they (AMH) have plenty of experience getting those type trailers on and off.
My look at the fares table is that Haines to Skagway will $3.30 per foot of total length - with a 25% surcharge if the vehicle is 103 inches wide. I've been told but cannot verify that things like the awning mounts are measured to calculate width.
You should call them - 800-642-0066