eSata is generally a little faster. Sometimes not in 'peak' but generally in sustained or average speed. It also has a lower CPU impact.
However eSata is pretty much a dying standard. It has gone from commonly supported to not very commonly supported.
You are more likely to be able to easily access your files on future computers if you stick to USB. I'd suggest you get a USB3 enclosure as they are the same price, backwards compatible with usb2 and if a future PC needs to access the files you'll appreciate the higher through put.