For most riders, I would advise riding to Prince Rupert, B.C. and taking the Alaska ferry north from there. Our ferry system can be found right here: AMHS
And you can find a PDF copy of all the schedules here: 2013
But I know you like to go exploring and you've already been to Alaska once, so let me suggest another route that you might find more interesting. That would be to ride out to Port Angeles, WA (or ship your bike to Seattle again and ride from there if you will be short on time). Take the ferry Coho from Port Angeles to Victoria, B.C. (a beautiful city) then ride north on Vancouver Island (you can find several ride reports here on ADVrider describing that trip) to Port Hardy. From Port Hardy take a Canadian ferry to Prince Rupert, and there switch to an Alaska ferry for the remainder of the trip to Skagway. While at Prince Rupert, you might be able to spend a day or two riding inland up the Skeena River and maybe even south on 37 to Kitimat (inmate kildala2000 lives there, I believe) or north to Hyder, AK.
You could have a pretty good vacation before you even reached Alaska.