When in Alaska and Canada, we stayed for a week in Haines at the Oceanside CG. Right on the water and next to downtown. Tight back-in spaces but great views and nice folks running the place. Take the ferry over to Skagway if you like. We enjoyed Haines for the laid back atmosphere and there are lots of things to do there. Cruise ships do come in a couple of times a week, but nothing like Skagway.
While in Haines, the wife and I were not totally certain just how we were going to journey south. The ride into Haines, like Sue said was beautiful, as is leaving from Skagway. What we did was to take the Alaska ferry system to Prince Rupert, BC, which stops for several days each at Juneau, Sitka and ketchican. It was expensive but great.