((OK, I'm back, and i'll assume that Greer went with Gilam, Deac, and co.))
*some time between when the battle with Duncan ended and the gliders took off Greer pulled the bolt off and applied some bacta to his arm, and picked up his sword.*
*On the glider, Greer pulls out his sword*
Greer: we can take them now.
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.