*Matt wanted to choose his words carefully now*
Matt: I think it'd be better if both of you cooperated in giving me the crash-course. The only negative side I see would be if you guys started fighting over how to train me, but apparently you'll do that anyway. When we landed I really thought I could manage without training, but with the invincible zombies, giant cats, half-zombie chick, and the rest of them, I'm not so sure right now. Now I'd usually decide to stay back, but I want to pull my own weight around here, and from the way this war is going, staying here could be more dangerous than going in. So I say just agree to train me on a certain weapon and a style for fighting, get me some of those special warming clothes, and just give me the best advice you havae.
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.