I've owned a bunch of Vaqueros and most of mine shot low and left but some were dead-on windage-wise. I credit this to Ruger improperly clocking the barrel if done after the front sight was installed, or not installing it straight up in the first place. I can look over the top of some of mine and see clearly it's not installed straight up. There are a few work-around. First off, though, they all shoot low until you file the front sight down for the load you want at the distance you want to sight it for. It's best to do this last after load development. Getting back to the windage issue, some will claim is all the shooter's fault or how you hold it (or whatever). I've owned and shot enough and experimented enough (e.g., trying different grips, including big hand-filling ones) to know that it's not me, especially when some are off and some aren't. If you determined you're not causing it and want to correct it, you could hook up with a competent local gunsmith with proper vice to reclock your barrel. This would be trial and error. Some can even mount it to their truck and go to the range with you! He might need to further address barrel-to-cylinder gap, though. Another popular way is to replace the front sight with a dovetailed windage-adjustable sight. I find these "unsightly" IMO (no pun intended!). Another way, albeit risky, is the route I've taken, and that's by hitting the barrel with a rubber hammer while the sight is laying against a hockey puck. I cover each with thick paper to protect the finish and do it carefully. It's also trial and error and usually requires minor changes each time. You could also send the gun and your target back to Ruger and I think they can help correct it (might be the best option for most). Lastly, if you only have one Vaquero, you could just get used to your sight alignment by making the front sight align to the inside-right or inside-left with your rear sight when shooting. I used to do this until I acquired too many Vaqueros. I suspect most owners just do this.
After you find the load the gun likes best and decide on a distance you want that load regulated to, then file your front sight. If you use a flat bastard, measure the sight height and go slowly (again, trial and error).
In the end, you'll probably want to keep it and might even elect to have an action job, base pin, custom grips, etc. They're capable of great accuracy given the sight radius and practice. The good thing is that they do have fine sights. (I hate 0.125"-wide front sights on short barrels!)
Edited for typos.