You may be out of luck there. The Big Three American carriers (United, Delta, American) just raised the minimum age of unaccompanied travel from 12 to 15. You are required to book their unaccompanied minor service for an extra $150 (DL+AA). Given that they all seem to have raised in unison is probably not a coincident, but who knows.
You can try some alternative carrier, if they are available. Apparently Jet Blue allows 14 year olds to fly alone.
If you have to book the unaccompanied minor service, the airline will tell you what you need to do.
When our underage kids were flying solo, we never gave them any additional documents and it was fine. To be safe you can give them a letter that states purpose, time & date of the trip, authorizes your brother to make decisions for your kids and authorizes the kid to travel alone.
Unless your son is an experienced flyer, it's probably a good idea to go step by step through the process. Check in, how to read a boarding pass and to identify the important information (gate, boarding time, gate cutoff time, flight number, etc.), doc control and security, map of the departure airport, etc. There is probably a suitable youtube video of that airport you can watch together.
Stating the obvious: Non-stop flights are easier than connections. "Direct" is sometimes not enough, you want "non-stop". Make sure your son has a cell phone and it's charged before heading to the airport.
My question is what documentation should I provide for my brother in case he's stopped or questioned for some reason? Would a note from me and my wife with our contact info and an explanation that our son is allowed to be with his uncle be sufficient?
You don't need one, but it's good to have one just in case.
My son has a passport, but will he need any other documents to fly home alone when he gets to the airport?
No. Passport and boarding pass is all that's required
Could my brother get permission to accompany him through security?
No. Your brother may try to get a so called "gate-pass" but since the airlines want to make the extra money for their service, it's very likely that he will be denied.