I would definitely do the cruise at the end, not the middle. I feel like switching from resort to resort will just be simpler than going from resort to boat to resort.
I voted for the Contemp/AKL/Cruise option.
I have not stayed at the Contemporary, but I have spent a lot of time there. I have, on the other hand, stayed at AKL, and it was my favorite resort stay. I still get the warm fuzzies just entering the place. Love the lobby, the restaurants, the gift shop, the activities. It feels like a magical hideaway in the middle of bustling Disney World.