From what I've heard, the Valve-released Half-Life: Source is a pretty half-assed port. I don't know if it affects anything mechanically, but if you have the original game as well, I don't see any reason not to play it instead. Obviously Black Mesa: Source, being a full-fledged fan remake, plays quite a bit differently to the original.
Speaking personally, I generally like to play the original versions of stuff the first time through if at all possible, just to get the same experience that people had when it was brand-new. It also helps you gain a better perspective on just how much fan-made projects like the SCP and FSU have managed to accomplish.