I've noticed the Winchester 7.62x39 has a large rifle primer and Remington has a small rifle primer.

Does it matter either way?  Is one better or worse?
Which does Federal use?

Does Winchester, Federal, or Remington actually make their own 7.62 or is it actually made by someone else for them?

For reloading, is one better than the others?

All are large rifle primer except Remington.  I have a Ruger M77 7.62x39 in which the firing pin hit is a tad off from center...with it, I have experienced a failure to fire or 2 when using Remington brass for reloading.  Since I deer hunt with mine, that is no good, so I use large primer cases.  In my Ruger Number 1 in 7.62x39, both small and large primer cases fire fine.  I also have about 20,000 reclaimed USGI 30 carbine primers ($6 per 1000), so I use the Remington cases with them for practice/plinking.  

So, other than my rifle pickiness and the fact that I have lots of small rifle primers to use, for most people I see no practical difference between small and large primer cases.  I have no idea of who makes the ammo for those companies, but suspect they all make their own.  I do note that the brands of brass weight differently, but have seen no impact point differences with my reloads up to 150yd (the length of the range) when using the same bullets.  

SAAMI has made the large rifle primer the spec now so you should see everything going to that.

Do you care to give a heads-up on where to buy the reclaimed carb primers at $6/K?

I would recommend doing the exact opposite of whatever Winchester does to their ammo, as its probably the shittiest 7.62 I have ever seen.  Bought a box from walmsrt a while back, and while loading it into a magazine, the bullet fell into the shell like 2 mm, leaving a short stub sticking out.  I have a picture of it somewhere that I will try and find.

I reload both the small primer RP cases and Winchester/PMC/Federal cases using the same load recipe except for the primer of course.  All went bang in my MAK 90's

I was asked about the reclaimed primers.  I get them at the Knob Creek machinegun shoot.  On the left side of the road going towards the pole barn is always a dealer that sells surplus ammo and components out of his van.  $7/1000 or $6/1000 if you buy 5000.  Always a sucker for an ammo component bargain, I tried them and bought more my next trips.  He still had then at the October show.  I do not recall his company's name.  Between 4 of us, we have brought about 50,000 of them.  Glance at each to make sure the anvil is present and not squished before loading.  About 1 out of a hundred were deformed and had to be tossed.  They came from demilling USGI 30 carbine ammo.