"NYPD lawyers proposed a new tactic, the TEI, that allowed officers to monitor political or religious speech whenever the “facts or circumstances reasonably indicate” that groups of two or more people were involved in plotting terrorism or other violent crime." and

"Doing so allowed police, in effect, to treat anyone who attends prayer services as a potential suspect. Sermons, ordinarily protected by the First Amendment, could be monitored and recorded." and also,

"And under the new Handschu guidelines, no one outside the NYPD could question the secret practice."

While I agree that the NYPD explicitly hasn't labeled all mosques, the laws mentioned above allow them to treat all mosques as potential trrorst organizations. And no one can question them.