Depends on what you're using it for. If it's a flash drive/small external, USB 3.0 for sure due to it's backwards compatibility with USB 2.0 and it does offer powered connection (enough for most 2.5" Hdds). But if it's an external HDD, I'd go for esata because you get higher sustained speeds which is REALLY nice when transferring large amounts of data.
But if you don't do a lot of large data transfers, then I think USB 3.0 wins. Then again, I haven't seen any benchmarks of esata on a 6Gbps connection.
Semi-related, if it was USb 2.0 vs esata, I would for sure go with esata (ofc with a backup USB connection encase you have to the drive on a unfamiliar computer that may not have a esata connection)