eSATA will yield the full speed of the HD
USB3 with a good controller will yield the full speed of the HD
USB3 with the controller integrated into the chipset (Intel Z series motherboards) will top out ~500MB/Sec.
Many eSATA controllers top out at ~250MB/Sec
If you use an eSATA port via the SATA-III controller integrated into the chipset, you can reach speeds up to 600MB/Sec.
No single conventional HD is close to saturating SATA-II (300MB/Sec)... so for single HDs it's pretty much a moot point.
If you're connecting a fast SATA-III SSD, it makes a *HUGE* difference.
If you're running two/four external drives in RAID-0, the controller (USB3 or eSATA) makes a huge difference.