Neither FBI nor Pentagon have ability to fly drones in the US airspace at will. On the contrary, they, like everyone else, have to get FAA approvals and those always leak. And usually in fact published by the FAA who needs to warn pilots of potential threats -- one could go to the official FAA website and search those NOTAMs.
Ignoring FAA by the FBI or the military just doesn't happen, the price to pay is WAY too high.
NSA or spooks could theoretically be behind this, but why do it where it annoys people and attracts attention and not in some desert or foreign place? Something doesn't add up.