I have a 09 is250 and was wondering if the fsport exhaust would make me fail my emissions inspection in ny?

 

No, you should be fine.

 

axle/cat back exhausts dont change the amount of emissions

 

CAT back may be involve to emission due to secondary CAT deleted. For our car, if you don't have second CAT (in CA) you won't pass smog check, i'm not sure about NY.

But for F-SPORT EXHAUST, you won't have any problem

 

No it is 50 state legal. Most aftermarket items made by the car manufacturer itself like TRD make them to be able to pass smog. As long as that's the only part you mod on the exhaust. When you start deleting the cats or do hi-flow cats thats where it becomes a different story.