There are local car rentals in "downtown" Brooklyn even in the Brooklyn Marriot. All the majors have them. Hertz calls them HLE or Hertz Local Edition and I've used them for rentals. Avis and Enterprise also have them and it is a simple Uber ride to the port. Hertz at 92 Boerum Pl, Brooklyn, NY 11201 is only 2 miles away from the Brooklyn Port for example.