Well, I was faced with the same decision as you a few months back. I bought a 4 5/8" stainless Vaquero in .45 Colt and haven't regretted it. In fact, now I own two, one with 4 5/8" and one with 5 1/2" barrel.
I handload though, and if you don't then there's a more limited supply of heavy hunting loads for the .45 Colt (and they're more expensive) than for the .44 mag. I've shot both though, and the .45 sure seems to kick a lot less (even with very heavy loads).
I chose the Vaquero because I like the fixed sights. It's a little harder to sight in, but once you're there for your hunting load, it stays there. I can compensate for plinking, and it's only slightly.
FWIW
~Rat