Given that, why would anybody be "astounded" about the NYPD spying on potential trouble-makers? I'd be angry if they weren't spying. See The Week article on Yahoo News about this.
Large city police department intelligence units have kept an eye on malcontent groups for at least 80 years. I'm sure the practice is older than that, going back to when anarchist, abolitionist, prohibition and IWW groups were violent threats.
Getting technical assistance and training in tradecraft from the CIA makes perfect sense. Who knows more about these things than they do?