Matt: No, we don't. We don't have any idea where the magic came from, what it's supposed to do, wether it's dangerous or not. We don't know who had us kidnapped, why they had us kidnapped, and wether or not what they're trying to do is dangerous. All I know is that someone had us kidnapped, and wants to do a ritual on us that may very well cause the destruction of the universe.
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.