I'd second taking the ferry system. Most of the SE Alaska towns aren't accessible by road - I think only Skagway and Haines. And of course all the coastline and inside waterways are only accessible by water. On a cruise ship you will see a few scripted sights, but you won't really see Alaska. Ketchikan, Juneau, and the make-believe part of Hoonah don't count. Most of Sitka, Petersburg, Wrangell, Pelican, real-Hoonah, Kake, Meyers Chuck are more real. But to me it's really about the scenery and wildlife. Our experience is all coastal by boat with the exception of a road trip from Seward up to Denali, and a bit of exploring from Valdez. We are anchored off of a waterfall right now, watching bears catch and eat salmon.