I was there
I was just getting in from a Red-eye and had a connection I was waiting on to get home.
We were actually in the remote Jetblue terminal. The terminal in which you have to take a shuttle to for gates 18 - ??.
The flight crew had just gone down the jetway and I was called up to pre-board (broken ankle), when the flight crew came back up.
An announcement came at the gate that the flight was being held by JFK operations and nothing else was known. I immediately said to my partner it was likely security related since they pulled the crew off.
About 5 minute later a general announcement came over that the building needed to be evacuated immediately. We walked over to where the shuttle loads/unloads and suddenly the doors were closed and we were kept inside.
It was obvious the "security" (not TSA) in this building had no idea what to do. Another announcement came on to evacuate and pax were getting angry that the doors were being blocked. They opened the door and everyone started filing outside - problem is we were in the middle of the ramp area.
They did get 2 shuttles away before telling everyone to come back in the building. They had no information and provided no updates.
Most of us got our updates from friends who happened to be watching Fox News because Geraldo Rivera was in Terminal 5 and had been evacuated.
Our flight was held at the gate because it was unknown if any of the pax for our flight had boarded the shuttles which went to the main terminal as those pax were forced to exit the building and re-enter through security.
It wasn't a big deal -but it was obvious that if an emergency really did occur that the security staff had no idea what to do. They were all yelling over top of each other on their walki's and no one was running the show.
Pretty scary also considering it is NY.