Like they have said before and I fell into this last year arriving FLL at 11pm and taking a taxi to downtown Miami. I dished out about $80.00. This I would not do again. Find out more about the shuttle.
We are doing the same thing. We rented a car at the FLL airport and are returning it to the Miami Airport and the rental car place at the Miami Airport takes you to the cruise ship at no cost. We have done the cab from FLL to Miami but it is expensive and if you have more than a couple of people you'll have trouble getting a weeks worth of luggage in a cab. Hope this helps!