We have used National (once) and Alamo (twice), picking up at the car rental center at MIA airport and returning the cars to the Alamo/National location at the Dolphin (twice) or MCO (once, after keeping the car for our entire stay that included a stay at Vero Beach after the WDW portion of the trip). Although Alamo/National has a shuttle from the port, we preferred to use Lyft after our cruise last January, but there were just the two of us, so it was pretty reasonable, about half the cost of the taxis we used the first two times we did this.
Alamo/National charges $3.95/day as a convenience fee for the toll services, charged back to the credit card on file for the rental, typically about 4 weeks after the rental in our experience. The charge is only imposed for days on which you incur toll charges, so only one such charge if you drive up to WDW and then return the car.