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Guarnere had been woken up and mysteriously been instructed to report in to Elaina. He thought this was strange, but it was not unheard of so he followed the orders. He went to the detention block, and found her there, escorting some recently-captured Republic troops.
"What did I miss?"
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.
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