O'Connor: You might try the waiting room, he can jack into his office from there
*Greer opened his datapad in his computer and checked up on the senators. They had already cracked one's account, and they had only found out a little. He checked up the senator's message box, and found authorisation for a team to be sent to the hospital. He quickly checked the NRI office for teams on request, and found the one he wanted*
Greer: *THrough comlink* Heads up, we got Team Foxtrot coming in.
O'Connor: Oh crap.
*He got his rifle out of the case and assembled it swiftly, adding a silencer to the tip.*
O'Connor: You should be able to help us by slowing them down, but you can do whatever you want, just don't get in the way.
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.