Anything around the Brooklyn Cruise Terminal would most likely cost the same. Cheaper options do exist, but would require additional travel via cab rides, so the additional cost has to be considered.

One option that I've know of people doing is using AirportParkingInc.com to book a parking reservation at a hotel nearby LGA or JFK. Apparently, they've set up agreements with hotels so that those who need to drive to the airport can park in their hotel parking lot for a fee and take their free shuttle to the airport. These fees are typically much lower than the "standard" airport parking fee.

A co-worker of mine who lives in Upstate NY needed to get to JFK for a 10-day vacation and paid $10/day (plus a small service fee). She was telling me just the other day that her friend decided to go directly to the hotel manager recently and got an even better deal.

Also, call the hotels around the area. There's a Marriott and Sheraton in Brooklyn that have parking lots. Maybe it's cheaper. Be sure to mention that you won't be staying at the hotels when your car is there.

YMMV. It is a trek to go from the hotel to the cruise terminal (although I imagine the hotel will help you get a cab), but do some research to see if the savings is worth it (remember to add in cab fare!). If I were traveling with a family and need to drag a 3 year-old along, I may just park at the terminal. But if I were with my buddies, we might set out for an adventure.