@Alex Since I had never considered that, I decided to look it up. Seems both technologies are fairly recent, so neither is being used to its fullest capacity. It looks like SATA III should be faster, as USB 3.0 maxes out at ~5 GB/s, but in reality, most HDDs only use SATA III at around 5 GB/s anyway, so they pretty much break even.
The only concern I found is if you have multiple 3.0 ports on one card, most only use one PCI-e lane, so using more than 1 at a time will divide up the maximum speed to each port. With that in mind, and my tendency to avoid complicated scenarios, I would have to say internal is more reliable at the moment.