Mineola is definately a top spot for railfanning. You've got OB, PJ, Ronkonkoma, and Montauk line trains going through there. And you've also got Nassau Tower as something to have in your shot too.
And a little suggestion, ride the FBA line. It's really fun. Be sure though to get the RFW. If you get stuck with an M7, then it's really not much of a thrill. The tracks practically hang off the el structure
As for the cops, they can be anywhere, at anytime, and with any kind of intention. I took a shot of a train leaving Patchogue right in front of a few Suffolk County cops, no problem. Same thing at Jamaica with 2 MTA cops. I've been stopped at Mineola for taking pictures by an MTA cop, but easily explained to him that taking pictures in fact IS legal. My friend was stopped at HPA by 2 MTA cops, but he didn't argue it. Then there was that whole state trooper incident at Ronkonkoma. That guy would not let up. Same with the 2 MTA cops who stopped me on the PW line for filming.
Basically, it's the luck of the draw.