You have to change boats in Juneau to catch the one headed to Whittier. It, the Cross Gulf ferry doesn't run very often and is/ was summer only. It isn't very popular with tourists as it stays a long way off shore on the run. If a person wants to stay out of Canada, this is the only ferry routes that will accomplish this. The only other way would be to put your RV on a rail barge in Everett Washington and you fly up to Anchorage to pick it up.
On my web site I have our last trips cost from Prince Rupert to Skagway, under Alaska 2011 heading. This would give you a figure to probably triple the figure. I would guess you are looking at $1500 and up each direction of travel.
I have also done the Skagway to Bellingham run previously. Don't remember the cost and I am away from home, in South Dakota currently, so don't have access to those figures.