Thunderbolt is just as fast, or faster, than the internal SATA connection. I don't believe it has any latency issues, so it should work perfectly for an external boot device. I think USB 3.0 would work, depending on what speed the Mac and HDD can negotiate to. And of course eSATA should be fine too. I would skip USB 2.0 - too slow for the increased speed of an SSD to be noticed. Regarding gig-e ethernet, like in an iSCSI SAN, it's possible, but I'm not sure the Mac supports booting from it...?
I have a 2010 iMac with only USB 2.0 ports - I want an SSD to boot from but no cookie for me. 🙁