Both disappeared roughly around the same, from what I understand, and that Serana was the one who ended up walking in the front door. Also, finding a daughter of coldharbour is probably extremely hard, as only a few out of ~1000 survive the ordeal, so his wife and daughter were really only his options.
Again....
Valerica put her plan into motion because Harkon was going to sacrifice Serana. It was to protect her daughter more than it was the Elder Scrolls.
But back then, Harkon still had his wife to use, so why was Serana his first choice when he and Valerica hate each other? He could have detained her, fulfilled the prophecy, and been home for a glass of blood with little problem.
There is no conceivable reason for why his daughter that he loves would be his first choice instead of the wife that he hates, who hadn't disappeared on him yet,