"We could be outnumbered." Said Dag. "For all we know there's hundreds of them out there."
"Kid's got a point Dag." Said the Corporal. "We need to find out what these guys are capable of."
Dag sighed. "All right. We'll fight."
As they left he gave one last glance at the monitors. The aliens were overwhelming the republic forces. He hoped the squad was ready to handle them.
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.