You already answered your own question! NY will allow you to swap a different motor in as long as it passes the emissions standards for the year the of vehicle or anything since then... so if you get an 04 or newer motor with the ECU and all the emissions equipment (and make sure it\'s all happy), it should be legal. As far as I know, it doesn\'t have to be the same brand motor either, so you could drop in a motor out of an \'09 Corvette ZR1 if you wanted! 8-)
The easiest way to find out for sure though is just call the DMV in Albany and ask, I\'ve found they\'re very willing to help answer all kinds of odd questions.