Even though NYC roads can be interseting to say the least, I recommend flying into LaGuardia. The car rentals are a few minutes away by public bus or by shuttles. From there, it's a simple one road trip on the BQE (Brooklyn Queens Expressway). Prolly about a 20 minute drive.
Driving in from Newark would blast you with bridge/tunnel tolls that will break you before getting into Brooklyn. On top of that, the commute would be a good 2 hrs even with decent traffic.