Greer just contacted you w/ a location for you to meet up with the ship and trade the hostage, and, if it's still on, help with the assasin situation. And yes, I am doing this for the conflict it will result in with the new guild's price on Flax's head and Greer already having paid the Vilnovs to not kill him.
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.