"But we're not in their forest. We're in the bandits' cave!" Said Crem, choosing to forget the fact that he was agreeing with an elf. "We asked them for help, they said no. They could have done something about it years ago, but instead they wait until the fight is going on, and we've defeated most of them to act!"
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.