Car rentals close at 12am so you should still have time to get to the counter to get your car. It's just across the street from the main terminal.
I called Alamo, Enterprise, Avis, and Budget to book reservation. None of them are able to accommodate but Avis said they will put in a request since it is after hours with my after 11 pm arrival. Only Avis and Budget have drop-off locations at the Port Canaveral cruise terminal, it seems.
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