We had the same problem, we love Disney but we love to Cruise also. last trip we flew in on Saturday rented a car, stayed at POFQ 2 nights drove to Port Canaveral and did the 4 day Wonder, (parked the rental at the lot for $28) we had total control of our luggage untill we gave it to the porter at the ship.
After the cruise we picked up the car drove back to the Contemp. and stayed for 3 more days. We got our disney and cruise fix.
We had a great trip.
When we cruise even if we go through miami we always fly into mco and do WDW for 2 day before, drive down to the port and drive back to mco. We figure we have already paid for airfare might just as well get the most out of the trip.
We do think it is better to go to WDW before the cruise so you can relax after all that walking.