Both engines are pretty much bulletproof as long as you don't start running boost through them. The 3.7 is a touch faster at most road courses, but the 4.6 is also quicker down a drag strip, and has a more accessible aftermarket. The 4.6 has a more attractive exhaust note, in my opinion.
2014 Mustang V6-Built to run TTB, CAM-C, and ESP
Proving to my fellow racers that the disdain that some GT drivers have for V6 drivers is unfounded, one results archive at a time since 2013.