I am a travel agent and my primary areas are Disney destinations and cruises. I think that it will be most flexible and the best value for your money to do your cruise and Disney World separately. You will have a lot more options for your hotels - be sure to stay on-site at one of the Disney hotels - and prices will probably be better on a package. Be sure to allow at least 2-3 days to see each of the theme parks at Disney World - Magic Kingdom, Epcot and Animal Kingdom.
Please feel free to e-mail me if you have any questions!