Get a good file, a bunch of rounds, a black magic marker and go the the range. Shoot and and if you're low file a bit off the top of the front sight. Check point of aim. Shoot and file, repeat as necessary until you're where you want to be. Go slow, it usually doesn't take much. The marker is to blacken the top of the sight once the bluing is gone. Cold blue when you're finished. Oh, and it's wise to maybe put a layer or two of tape on the bbl. as files have a tenancy to slip...don't ask me how I know this.
The above assumes that it is in fact the Vaquero shooting low and not your shooting. I'd begin the whole process by shooting a lot until you're positive it's the gun and not you. Good Luck.
The Preacher