If you are running out of breath at the top end, then I would suggest an offroad pipe. But then again, you would have upgraded your exhaust by this point.
If all you have is a Thrasher CAI and you've decided to blow money on either an offroad pipe or a high flow cat, I would buy the high flow cat. The high flow cat should not affect your emissions.
In my opinion, you'd be better off doing other things with the $$ than blowing it on a high flow cat or offroad pipe. Neither are a good bang for the buck kind of mod...especially when your engine is pretty stock.