For one of our trips to Alaska we took the ferry from Bellingham, WA. It was a very pleasant ride and unlike the big cruise ships it goes through the narrow passage for most of the way - just one section of open water and that was traveled at night. We made stops at Juneau and others, including Ketchikan (loved it). At Juneau there were small vans waiting if you wanted to tour Mendenhall Glacier - recommended. The tides were just right which doesn't always happen so we were able to ride down a different waterway. When we were nearing the tiny town the townsfolk ran down the hill to the water so excited because they rarely see the ferry. The captain stopped and we were so close that conversations were flying back and forth. It was a neat experience for us and for the townspeople.
The ferry is the only means for some people to get from place to place. We even had a whole football team come aboard at one stop and they were off to play another team at another stop. It was great talking to the natives and finding out about their lifestyles in such remote areas. Santa even travels by ferry.
We got a room (extremely tiny) and we wished we didn't. The lounge chairs indoors were very comfortable and that would have been sufficient for us. We got off in Skagway.
Since you have a long period of time for your trip, I'd advise driving back rather than the ferry. Both ways are so different and enjoyable. In fact, you might consider driving up to Alaska and the relaxing ferry for your return. The quietness and easy time would be welcomed on your return. Driving up you will be so excited for the trip and more animals will be along the roadsides early in the summer. After touring Alaska you might not be as excited when you drove back on the highway. Just a thought..... Enjoy the planning.
Get the Milepost for history and maps but get Mike and Terri Church's book 'Alaskan Camping' for all the campground/RV park and boondocking site information. It includes the Yukon and Canada, also. There really aren't that many roads to drive so getting around is easy.
The only camping reservations we made when we drove up and back on another trip were for the July 4 weekend (Alaskans like to camp, too) and for 5 nights in Denali's Teklanika campground - the farthest you can drive in Denali. We only make those a couple weeks prior when we could better judge when we'd be there. As it turned out we got into the Denali area early so on a whim we boondocked nearby at a lovely spot the previous night and drove into Denali early the next morning and easily secured an additional 5 nights in Denali's front campground, Riley Creek for our 40' motorhome and Jeep. With 10 nights in Denali we saw 'THE' mountain 7 of 10 days and saw every one of the big 5 large animals living there - many time after time. It was an awesome stay. We were in Denali mid-August and the color was just starting to turn and the fireweed flowers were gorgeous.
Bottom line - don't make a lot of reservations for camping. If you pull in by 1pm or so you'll get a site.