Also make note that it would be EMPTY. A manpad stationed on the turnpike in the breakdown lane could hit a jet taking off from Newark easily. Blazing hot engines throttled up for takeout make a great heat signature. A 747 casually putting around NYC, not so much. Besides, AF1 has anti-missile tech on it.
I was only taking a guess. But ....
Whenever the president's 747's land or take off anywhere, security is there weeks in advance securing the area and flight path.
Maybe to a terrorist, the downing of one of the president's planes would be of great symbolic value, more so than killing hundreds onboard a commercial 747, and it would be worth spending that one missile they got into the country, and even worth getting caught. Or, even a large gun that was assembled in a Jersey City mosque from smuggled parts.
I do realize that they carry anti-missile technology, but having this large, fat aircraft flying low and slow repeatedly around a small area .... presents its own problems.
Again ... I was just guessing.