They got the ship well offshore before the President got anywhere near NYC. They never say where the other 4 ships were that they checked out based on the intell information.
I thought I heard yesterday (or was it this morning?) that there was another ship being searched out on the westcoast, possibly northwest?...maybe?
Anyways, if my geography is correct, Newark is only about 8-10 miles from Manhattan and a little inland. In fact, wouldn't a cargo ship have to scoot by within a mile or two of Manhattan in order to get to Newark? Under the Verazano Narrows Bridge? Six miles out to sea would put the boat closer to Manhattan than Newark.
I think what I'm getting at is after watching the special on the President's and his staff's movements on September 11th 2001, I just can't see the risk of putting the President within 6 miles of a "possible" nuclear threat, wind or no wind.
With all that said, my mental mapping could be all off and if so, my apologies. I appreciate your valuable insight none-the-less. :-)