It comes with “federally compliant catalytic converters”so why not? You are not in CA but best to ask the companies doing the swaps like AMW or Rubi. Mine will go through it’s first one in January but I am expecting more grief for the tires than the engine here in MA at least. heck my dealership who sold me the truck but didn’t do any of the mods still fixed some small stuff under warranty post HEMI swap, lift and tons of undercarriage battle scars. But check with the swappers as they have customers in all states
My understanding is that a motor swap is not technically illegal in New York, it comes down to how and when the emissions inspection is done.
All emissions inspections are done by local shops and they have a strict set of rules to follow. There has to be no check engine lights for emissions and all OBDII emissions monitors have to show a "PASS".
The rub will be if the local garage that does your emission inspections pulls back because they do not like if there is a VIN mismatch and/or if your swap while it does pass the ECU emissions related for that motor, does not show a pass for the emission systems your original motor would have passed but is not supported by your now new motor.
Also, if your local garage that does your inspection was to do a repair to a emissions related items, they are by NY law suppose to only use OEM or California CARB approved related emission repair parts for that model. So for example if your vehicle came with the Pentastar from the factory but your now HEMI swap needs a new CAT, they are supposedly only allowed to put in a Pentastar CAT as came from the factory and not they new HEMI related CAT. In practice, there is many repair shops in NYS that will sticker slap so long as you have no CEL and call it a day but they run the risk of loosing their repair license for such things.
Basically boils down to being not so cut and dry and will be a YMMV situation.