I lived in NYC for many years and have flown in and out of JFK, LGA and also Boston Logan many times with guns. I have never had a problem at any of the airports, including when I flew out of JFK on September 14, 2001, when security was at an all-time high. I would not give it another thought.
As a NY resident you would have had the applicable permits to own the guns. Either the problem is with non-residents or NYC has decided to make the life of gun owners as difficult as possible since you've left.
Better safe then sorry, if I where flying with guns that I couldn't easily replace, I would spend the extra money to avoid NYC & NJ or find an alternative method of getting my firearms to where ever I was going.