The holding in Kyllo is based on the search being of a home, where the Fourth Amendment protections are strongest (“At the very core” of the Fourth Amendment “stands the right of a man to retreat into his own home and there be free from unreasonable governmental intrusion.” Silverman v. United States, 365 U. S. 505, 511 (1961). ) and the holding is narrow: Where, as here, the Government uses a device that is not in general public use, to explore details of the home that would previously have been unknowable without physical intrusion, the surveillance is a “search” and is presumptively unreasonable without a warrant.

I'd expect NYC to say "These vans are strictly for anti-terrorism purposes and if we see a bomb then you're welcome to cite the exclusionary rule from the safety of a non-blown-up courthouse", though that viewpoint will not command a whole lot of support on HN. I think it's probably a loser at the current Supreme Court on a drug case and would get a 9-0 with Scalia writing a florid distinguishing opinion from Kyllo if a terrorism case somehow made it all the way to the Supreme Court. (Amateur analysis here; IANAL.)