Oydman

Here’s how to do it:

1) Fly to Seattle (Southwest has cheap flights)
2) Catch the Seattle – Vancouver, BC shuttle bus (http://www.quickcoach.com) but get off at Bellingham, WA airport.
3) Find your way from the airport to the ferry dock near downtown Bellingham (http://www.dot.state.ak.us/amhs/index.html)
4) Camp on the ferry deck or pay extra for a stateroom.
5) Have fun along the way, and in Skagway.
6) Take a ferry back to Juneau – there are several to choose from up there – once your sightseeing is done.
7) Fly back to Seattle (roughly $240 one-way last I checked)

or reverse the itinerary and fly to Juneau first. You could also take VIA rail to or from Prince Rupert, BC and catch the ferry from there. Looks like an awesome ride through the mountains. There is some flexibility with the rest of the schedule, but the ferry only departs at a certain time a couple of days/week from Bellingham, so that’s your limiting factor.