It depends on whether you want to pay a premium for futureproofing.
Drives with a USB 3.0 connections are still a bit more expensive, and the USB 3.0 capability won't really benefit you if you plug it into a USB 2.0 port. So today, using eSATA would be best.
But within a year or two USB 3.0 will doubtless become ubiquitous, and some systems you may want to use your drive with (laptops, for example) may not have eSATA ports. For mechanical hard drives USB 3.0 should perform as well as eSATA.