Foley: Not much to tell actually, we were about to assault a weapons camp when the angels found out all that area had been "contaminated" with the bio-chemicals and decided to go recruit as well as gain some weapons. Anyway we attacked at the same time as the angels and everything was pure chaos. We blew up most of the weapons, but resistance had been heavier than anticipated, and better armed. We went in with 15 men and ones we took the camp we were 6, those nine men were killed by angels, not the targets. The Angels had us outnumbered by then and we had to surrender. They executed the commander and everyone was captured. the other 4 members decided to join the angels once they found out they were mutating, I acted as if though I was going along with them but ran the first chance I got, taking some weapons on the way.
Vader's wife was very pregnant when she died 19 years ago. All of a sudden a 19 year old who is very strong in the force and has a distinct resembalance to him in his younger days rolls in from Vader's home planet with his old Master Obi-Wan (Who was the ONLY other person preset at the time his wife died. And to boot, the kid's last name is Skywalker.
So in answer to your question, he knew Luke was his son because his name is Darth Vader, and not Darth Retard.
-Forum post on why Vader knew Luke was his son.