It sounds as if your ORD-NYC-HKG-KUL routing is on Cathay Pacific and your ORD-LAX-KUL routing is on Malaysian. Be aware that the Malaysian option includes a forced transit stop and deboarding in TPE. It also includes a LAX transfer obviously, and nobody likes LAX (esp. if you are returning same way and reentering the country there). On the strength of those two points alone I would pick the via-NYC option.