*Greer read the message and sighed. He opened up a new one to send*
From: N-R-I Delta
To: N-R-I Alpha
Situation agreed on. Protecting Deac @ Ackbar Memorial. Subject is in coma and cannot be moved. I will leave a team of 7 men plus two independents to gaurd him. I will attempt the extract, but I need a rendevous point.
Stairway B, Ackbar Memorial
*O'connel sees Rwos looking at the hospital*
O'Connel: ****, what's he doing staring. He's gonna get killed.
*O'Connel runs out to meet Rwos*
O'Connel: GET INSIDE, THEY'RE COMING! GET IN THE HOSPITAL!
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.