I don't think its Klaus because she didn't meat him yet at that point. Her baby was taken away because she was a young mother and they did not wan't anyone to know about it. I think it is somone from the Gilbert family.
He surely can't be Klaus, vampire can't have children, they're dead...!! Nobody knows and it doesn't matter, Katherine probably has been making out with everyone since she was human, and at that time she could get pregnant... Von who? One of the many fallen for Kath =)
Katherine had her baby before she met Klaus and Elijah because she had her baby in Bulgaria. This is part of the main reason she was then sent to England, because she had an illegitimate daughter out of wedlock and had shamed her family so she was made to go to England. She had her baby in 1490. And she met Klaus and Elijah in England in 1492. So obviously they are two separate times. The father of Katherine's child hasn't been said, but until now all we are suppose to know is that its not relevant to the storyline. Maybe the writers will one Tag say who it is but at this moment it isn't important so its not being said. The father of her child could NOT be either Klaus oder Elijah since they were in England and she had her baby in Bulgaria. Its just an unknown person. It obviously isn't Damon oder Stefan either since they weren't in Bulgaria either and Katherine met them in Mystic Falls in 1864.
I really have no idea who it is, but im gonna take a guess and say maybe Klause??? I only say that cos she's been on the run for over 500 yrs oder more, plus she never got her baby back afther the birth of her baby girl... So thats my answer... But it could be anyone, if they ever tell us Mehr about it... So my answer as i sagte earlier is Klause...