It is definitely NOT always rocky out of NY Harbor. It has almost always been calm.
The main thing in my worry about is the winds. The windier it is, the more motion you will feel. I've only had 3 cruises that were rough out of 27 and only one was out of Bayonne/NY. They are:
A 3-night cruise that was supposed to go to Halifax (without disembarking) and back on the Anthem. There was a storm out at sea and the ship went south instead of northeast. It was pretty windy and while I didn't see anyone getting seasick, you could hardly spend any time out on deck at all.
A 5-night cruise on Enchantment that went to Bermuda and back out of Baltimore. Going down was fine. On the way back it was stormy and very windy. Many people were curled up on deck chairs unable to move. Note that on the way down it was fine AND we were doing a B2B. On the next leg, a 9-night Caribbean cruise, it was completely fine on the way down and the way back. So it's just that variable.
The WORST I've ever experienced was on a 7-night cruise out of Long Beach, California on Princess, the Love Boat itinerary. Going down was fine. But as soon as we left the cove in Cabo and re-entered the Pacific Ocean, it was INCREDIBLY windy. The winds were coming off the ocean from the west and hitting us broadside. The ship was ROCKING. 50% of the passengers AND 30% of the crew were down for the count. My wife got sick, took the pills provided by the ship, slept that afternoon until the morning, woke up and was fine. That was the only time either of us have ever been seasick.
So, NY Harbor isn't bad at all. And it really depends on the weather as to any problems.