MacWorld published a great article comparing USB 3 and Thunderbolt real-world speeds for an external hard drive and an external solid state drive. It turns out that a SOLID STATE DRIVE connected via Thunderbolt runs faster, but with a normal external hard disk drive (spinning at 7200 RPM), USB 3 and Thunderbolt are nearly equal (with USB 3 running slightly faster). If you are considering a drive with two Thunderbolt ports, then daisy-chaining devices is possible and fast with Thunderbolt and not possible with USB 3.
For most of us, we are getting an external drive to store extra data that won’t fit on our internal drive. And that external will be a single, one-off drive that gets plugged in directly to the computer. In this usage senario, if you are considering moderately priced alternatives (i.e. hard disk drives and not solid state drives), then paying extra for Thunderbolt connectivity will not give you greater functionality; it’s probably better to consider a simple USB 3 drive.
Here are MacWorld’s conclusions (read the full article here):
[7200RMP Hard Disk Drive:] Thunderbolt turned in scores nearly identical to the USB 3.0 results, showing that the 7200-rpm drive was acting as a bottleneck to faster transfer speeds.
[Solid State Drive:] Thunderbolt was much faster on these SSD tests than it was with the hard drive, and it was faster than USB 3.0 in all six tasks, though to varying degrees.
What does it all mean?
While you won’t see a tenfold increase in the transfer speed from USB 2.0 to USB 3.0 in real-world use, USB 3.0 is fast—about three times faster than USB 2.0 with a spinning hard drive, and three to five times faster with SSD. And using a hub doesn’t impact speeds, even with other (and slower) peripherals attached. USB 3.0 is also faster than FireWire 800, and it stacks up favorably against Thunderbolt. Also, depending on the task and the drives used, it can be just as fast Intel’s speedy connection. When you remove the drive-speed bottleneck (by using an SSD), however, Thunderbolt can trump USB 3.0 easily.