Ok....i'll try to help if i can, is it EVERY ship that makes your SH3 CTD? if so it "could" be a pc prob, if not it could be a faulty ship or a faulty download
have you added anything to NYGM ie:- additional mods, if so that could be the cause...sorry can't help you anymore...i'm sure one of the NYGM dev team members could help you out.
If your game runs fine with other games, and SH3 with NO mods then chances are you have a faulty download
hope you get things sorted