Although there are computer and sensor changes over the PT Cruiser lifetime, as long as you use your computer, the minor internal changes will not be a problem, keep your intake manifold to match the sensors in it. Essentially, any PT Cruiser 2.4 engine block and head will interchange with each other. I have done a lot of parts checking and just about every part fits the 2002-2009 or 2004-2009 without fail. It's the computer that is the important part of the tune for your New York checks, just like California.
Only the 2004 motor is listed as a direct interchange. Of course the interchange manuals don't tell you what is different but you definitely want to avoid any pre-2003 motor and the crank position sensor/tone ring setup changed in 2003.