I did some fare checks on the ferry.
On the Columbia out of Bellingham Wa.It leaves Friday evening and it's 3 nights to Haynes Ak.. Reason to Haynes is that was our starting point on the drive to Denali. Or you can get off in Skagway,next stop 15 miles away by boat.
The fare for a truck less than 19',two passengers , inside two person berth,is just under $2,000. On the smaller ferry's we would sleep on deck but that is usually only for a night.
The trip to Haynes is 3 nights and there are more walk on people we have found that board in Bellingham. So it's harder to get someplace to set up for the nights on deck. There are free showers on board so that is a plus if you just sleep in the lounges,which will work but you have to remove your gear during the day.That isn't a problem as you get to visit your vehicle at times during the trip.Several times during the day and night. If you take a dog you need to go to your vehicle to tend to it.
It's something that can be done.But we still prefer the berth it's only less than $400 for the 3 nights.
IMO to ferry up is the best way as you don't have to worry about being back to the ferry terminal to catch the ferry.
Another way is to drive to Port Hardy up Vancouver Island to catch the BC ferry Northern Expedition to Prince Rupert it's about $700 same two people plus vehicle. It's an 11 hour trip there so you don't have to get a berth ,than get the Alaskan ferry there to other ports in the southeast.
We have done the BC ferry 3 of our trips because we had plans to visit places in the SE,so catching the smaller ferry's worked and took us to some great places.
Our last trip (check my blog) we had 5 weeks planned for the trip.With driving to Prince Rupert at the end of the trip to catch the ferry to Port Hardy,than drive the rest of the way home from there.
It's shorter time wise to at least ferry one way. Plus the trip on the ferry is great. So much to see and do aboard.
All of this depends on what you want to do in Alaska and how much time and money you want to invest.
I haven't done a comparison on driving both ways to using the ferry but gas is expensive through Canada and Alaska, so to me I don't even think about not taking the ferry. Although we drove 5,500 miles in and around Alaska,Yukon and BC and I think the ferry was maybe 3,000+ miles.
Ted did a trip there where he flew up than rented a small motor home for a week or so than had a cruise planned for the return trip home.
You could fly both ways with getting a rental camper for a your time there,if that is an option.
There are many different ways to doing a trip up north.
Hope I have been some help.
Frank