My vote would be to drive into Haines and then ride the ferry over to Skagway. That is what we did in our 2011 trip. It was actually cheaper to go to Haines and ferry to Skagway then driving into and out of Skagway. If you are lucky and can catch the daytime ferry, the 1 hour ride is wonderfull. Loading and unloading is a breeze, just follow the crew instructions as they have done this more than a few times.
Now then, keep in mind that Skagway is a cruise ship town. There will most likely be 4-5 cruise ships there at any given time. It's kind of interesting to see all the lemmings heading back to the ships in the late afternoon just before they all leave and a new bunch will dock in the morning.
Keith