It does kind of depend on whether or not you want to take on a new caliber or simplify things and stay with the .44 special and .44 magnums.
The 'old' Vaquero might become something of a collector item, I personally kind of doubt it but it could happen, so it depends also on if you're going to buy it to shoot it.
For some reason (maybe all the cowboy shows I watched as a youth) I always wanted a .45 Colt so I got a BH in that caliber.
If you're buying it to shoot it and like both equally (i.e. they both fit your hand just fine) I'd go with the Vaquero but it would be a tough call. The good news is, you really can't go wrong with either one.
I kind of hope Bob Wright or some of the other real wheel gun expert chime in here with their opinions.