Welcome to the boards, Andrea, you'll find a lot of nice helpful people here.
Being that we've done all three ways now, I would have to say it is more dependant on what you want to do.
If all you're planning on doing is going to WDW and then the cruise, the Disney transfers are the most painless as the luggage organization alone is worth it. They include tags for you to put on your checked pieces for the way down and they will bring them right to your room at Boardwalk. You do not have to claim them at the Orlando Airport. They will then also transfer them to the ship directly for you. Then when you disembark the ship there are airline pesonnel there at the cruise terminal to check you in for your flight on the spot (the last is included either way). I think Ginger's a bit confused, The bus service to/from the resorts to the parks is good, and I think she means going from resort to resort isn't the easiest to accomplish, but all the resorts now have a bus that goes to the ticket and trans center, and, you can always cut through Epcot and Use their bus stops to go to all the resorts and back.
The Limo is a good option and we used it last time in a hybrid manner for just the return trip from the cruise to the resort(we did it in reverse of you and rented a car 1 way to Cocoa Beach for some exploring the day before we cruised) and to the airport for the flight home. But this could cost a good bit more than the disney transfers.
Renting your own car for the whole time is also a good option if you're comfortable doing all the driving around between the airport, WDW and Cape Canaveral, and would give you the flexibility to do some stops, if you wanted to.