"Well, part of it is because I know you wouldn't be stupid enough to work under your real name, part of it's because your FBI profile is strangely classified." A pause. "But mostly, it's because out of the fifteen from Twin Falls, Teri's the one that most resembles you." He looked at the profile. "Mother's maiden name was Grant, studied at the FBI academy in D.C....." he kept reading the rest of her personal information off the profile.
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.