The "Vaquero" is what we now call the "Old Vaquero" and was discontinued in 2004. It was built on the large-frame, that is, the same 44Magnum-class frame as the SuperBlackhawk except with fixed sights. It was "overlarge" for most people wanting a "traditional SA".
The New Vaquero took over in 2004, built on a revival of the mid-size frame that Ruger hadn't shipped since 1972. The NewVaq of course has the transfer bar safety unlike the previous mid-frames. The NewVaq is very similar in size/heft/feel to a Colt SAA made after WW2.
The NewVaq isn't as tough, in some respects. When chambered in 45LC you're limited to the same power levels as what a Colt can handle, which is still decent but not the magnum-class 45LC+Ps that the OldVaqs could handle. In 357Mag, the other main caliber, the NewVaq can handle anything you can throw at it - the cylinder walls are still beefier than a Ruger GP100 or S&W 686 or other L-frame. There's also some limited-production runs of 44Special lately - and those wrongly got marked "Vaquero" when in fact they're mid-frame NewVaqs.
Now here's the kicker: the reason you want a NewVaq is that all six chambers were cut with the same bit/reamer set, in sequence. The OldVaqs were done on machines that did them all-six-at-once, which often led to variances between chambers. So the average out-of-the-box accuracy of the NewVaq is higher.
In 2007 or so the remaining large-frame Rugers got the new cylinder process, which is good. You can ID such guns via looking at the barrel - if the "read the manual" safety BS is on the underside of the barrel, you have the new process, while the warning on the barrel's side means old (not as good). Again: this only affects large-frames - mid-frames always had the cylinder improvements from the first (well, 2004 anyways).
One more detail if you're looking for peak accuracy: get the 357. When they screw the barrel into the frame, the thicker barrel walls of the 357 resist deformation. With the 44s and 45s you often get a "constriction" at the back of the barrel. The good news is, this is fixable. Either have a gunsmith ream the forcing cone deeper (a "Taylor Throat" job, or sometimes called a "Maxi-Throat") or do a bit of fire-lapping to grind down high spots using grit compound on some handloaded bullets. You'll have to google for more info on that - you can get kits with instructions.