I voted for Torres.
Scotty sucked! Sorry Scotty fans but it's true, when was he ever a shown to be a good engineer? He did an okay job but only seemed great because he flat out lied to his superiors.
Geordie was okay, my only problem with him was that he couldn't stop the warp core from blowing up under his ass, "There's gas coming out of the wall! The ship's lost, get out of here!!!" "Sir, shoudn't we try to repair the coolant leek or eject the ..." "Barrel roll!!!"
O'Brien is a guy I'd like to hang out with, but I don't see anything that makes him the best engineer.
Torres was a true miracle worker, she kept the ship running for seven years with no starbases nearby, she and her staff worked 24/7 to keep the plasma running and the gel packs healthy, she found a way to build irreplacable photon torpedoes and cranked out shuttle after shuttle in her spare time.