With the right external enclosure or USB3/SATA docking station, an external HDD or SSD will run as fast via USB3, as it does via Thunderbolt.
You didn't say whether you _have_ the HDD/SSD you want to connect yet.
If you don't, I'd suggest an SSD connected via a plugable.com USB3/SATA dock (NFI, just a satisfied, paying customer).
You want something that supports UASP (USB Attached SCSI Protocol) for faster performance on UASP capable systems (the Mac will take advantage of this).
BE CAREFUL -- not all enclosures or docks will have this support.