In many cases correcting a deviated septum can correct asymmetric nostrils but not always. It would require an actual examination to be sure, but if the end of the septum is pushing off to one side, that can be the culprit. I would make sure you see a doctor with both septoplasty and rhinoplasty experience. Good Luck!
Web reference: http://drpero.com/aesthetic-procedures/rhinoplasty/