The N4 would be the better choice if you really want stock Android, and if getting Android updates before anyone else/as fast as possible is also high on your list of priorities. Keep in mind that your menu, home, and back buttons are on the display itself with the nexus, so you're going to have a little less screen space at your disposal.
I'd go with the S3 but either is a good choice. My S3 is an extremely powerful, reliable, and efficient device. Never freezes or crashes and can handle absolutely anything I throw at it. Plus, it's been out for over six months, so there is a wonderful amount of accessories and developer support for it. While some people have their complaints, I find using the TouchWiz user interface to be a seemless experience. I'd also be very nervous about the all-encompassing glass material on the Nexus4 and the level of delicacy it instills.
At the end of the day you really have to decide what features are most important to YOU. Do you want a beast of a phone with a ton of accessories and enormous user community? Or do you want a monster of a device running stock android that's sexy as hell?
You can't go wrong.
Sent from my MetroPCS GS3