As it turned out, our boarding time was changed from 3:00 to 11:30 and then to 10;00, with the changes happening just days before our sailing. We left CT at 8:00 for a 2 hour trip. Traffic was heavy but for the most part wasn't awful until we got close to the port. It took an extra hour to go the last mile! Many side streets lead to the entrance of the port. They need better traffic control, more police at intersections. Traffic lights would change and you would go nowhere. Stressed drivers were blowing their horns, this did nothing to improve the situation.
We finally arrived at the parking lot around 11:00. At this point, I would estimate the lot was about half full. At the sail away, I got a good look at the lot, it was then approximately about 90% full. I would guess less than 100 spots left in the back. While this worked for our cruise, I can't imagine this current lot accommodating 2 cruise ships. There are 2 large dirt lots adjoining the paved lot. I don't know who owns them or if there are plans to make more parking there, but it seems that would be a likely solution.
I would not rule out sailing out of Brooklyn again but I would want to hear something has ben done to improve the traffic flow and parking if there is going to be more than one ship using the port.