Jokemaster walked in.
"What? That it. Y'know because of the last time you guys did your little experiment, I ended up being missing for 5 months, and my family had me declared dead. So I found myself jobless, family-less, only the 5,000 bucks I found scattered around the building you guys and Trent left me in, so I decided, you guys owe me a job, doesn't have to be something big, I'll help you program, set the machines up, etc. and you pay me, feed me, and all that.
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.