When I connect 2 PCs with each other through a 1GigE crossover cable and transfer large files (often larger than 1GB) through FTP, I often got transfer speed of around 70MB/s, which is likely limited by the hard drives and not by Ethernet's bandwidth.
I don't have a USB 3.0 device at hand, but we can safely assume that the limiting factor is still the hard drive's spinning speed (we aren't talking about SSDs here).
So, ceteris paribus, which protocol taxes the processor more (given the same transfer rate ?)