Ulna Shards Underground
*A man in another mask in the corner spoke up for the first time*
Man: I'm in.
*As the military moved in to blockade the planet, lots of others ships joined Greer's.*
Greer: Good, they'll be busy. Get ready to go to hyperspace as soon as we're free of the planet's gravity.
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.