Apple - repair an out-of-warranty Thunderbolt port

For that Mac, the thunderbolt port is a part of the motherboard (on the left, 3rd from the top):

So unless you're able to source the parts, perform a package exchange that clearly is a machine solder and then test things, the most economical repair would be to exchange the whole motherboard. As long as there is no physical damage inside, this would be a flat rate repair ($280) for Apple and probably cheaper than buying a logic board used. The flat rate repair would fix anything else wrong with the Mac. But, if you're up to reflow that part and do advanced soldering - there are lots of people that can attempt this repair even though it's not a trivial one.

While I'm sure it IS possible to just replace the thunderbolt port it would be labor intensive and a specialized procedure.

So yes, this is a replace the entire logic board procedure.

Apple DOES offer a flat rate repair service for out of warranty Macs though. They talk about it a little bit in their KB article - AppleCare Direct Mail-In Repair Serivce. You can get a free quote from Apple on the repair at https://support.apple.com/mac-notebooks/repair/service and it will likely be in the $300 range for parts, labor, shipping.

Basically they offer a flat rate repair. Assuming your Mac is damage free (no major dents, liquid damage, etc) they will mail it to their repair depot where the issues will be addressed and parts will be replaced for a flat fee. The fee varies between models/sizes but will more than likely be less than the cost of having the logic board replaced by itself at an Apple store or AASP.

If you don't like the web service option, you can also arrange this by calling AppleCare (1-800-APLCARE) or visiting the Genius Bar at an Apple store or AASP. You can find nearby Apple stores and AASPs using Apple's handy locate tool, just search for Service in your area.