You DO NOT NEED thunderbolt for the boot drive.
USB3 will be fine. I've been booting and running my 2012 Mac Mini for going on SIX YEARS now via an SSD sitting in a USB3/SATA dock. It runs as well today as the day I took it out of the box and booted it up.
For a ready-to-connect USB3 SSD, I would suggest either a Samsung t5 or one of these:
http://www.amazon.com/exec/obidos/ASIN/B00ZTRY532?tag=delt-20
Either 240gb or 500gb should do the job.
Or... buy a "bare" SSD and put it into an enclosure that supports UASP, or perhaps even a USB3/SATA dock or dongle/adapter.
USB3 (with UASP support) will give you reads around 430mbps and writes in the 300-350mbps range (depends on the brand and the size of the drive).
This is as good or better than what you'll get from thunderbolt.
Put the OS, your apps and accounts* on the SSD. Don't clog it up -- leave it "lean and clean" and it will run its best.
* -- put "large libraries" of movies, music and pictures on another drive. Since your internal drive may no longer function, you could consider attaching an external USB (platter-based) hard drive and use that. If your storage needs aren't great, you might even consider a second SSD.