It was authorized by the WH. Specifically, the WH Military Officer Louis Caldera. His statement...
"Last week, I approved a mission over New York. I take responsibility for that decision," White House Military Office director Louis Caldera said. "While federal authorities took the proper steps to notify state and local authorities in New York and New Jersey, its clear that the mission created confusion and disruption. I apologize and take responsibility for any distress that flight caused."
Of course, this is the same Louis Caldera who served board of directors for IndyMac Bank from 2002 until its failure and subsequent seizure by the government in July 2008. In other words, he was there for the entire housing bubble while the bank destroyed itself.
Apparently, the problem was that the WH informed certain agencies in the city and told the city if they made it public it would be a Federal crime. Working in Lower Manhattan for a large company, we get email messages all the time about various government operations/mass transit etc. If this email had been disseminated prior to 10 AM, noone would have cared or jumped. As it is, below is a copy of the email I received (note the time, after the flyover)...
Here's a link to the Post story about what happened. Big communication fumble here.
http://www.nypost.com/seven/04282009/news/...city_166544.htm