This answer contains spoilers… (view spoiler)[Pretty sure it was the Alderking. Since he vowed to kill his next child, Eolanthe probably lied about having a mortal lover and hid Jack with the Gordon family to protect him from the king. Obviously the "mortal lover" was not Mr. Gordon, so it wouldn't make sense to just never even hint at who the mortal father would have been. Also, there's the whole thing about Jack being an heir - can't be an heir with a mortal father. As far as the hint that Severin is familiar with Eolanthe, that would be explained if she was his father's longtime mistress. Severin is clever enough to have figured out that Eolanthe would consider herself too superior to have a mortal lover, and probably put two and two together, eventually realizing that Jack is his brother. Severin couldn't have been the father because he was asleep for hundreds of years prior to Jack's birth. (hide spoiler)]
This answer contains spoilers… (view spoiler)[I think it was Severin. There's a passage where Severin said he was familiar with Jack's mother and then Hazel thinks that the way he said it suggested that he was more than a little familiar with her. Then at the end when Eolanth (I think that's her name) is telling Jack about his father, even though he says he doesn't want to know, she say he knows already anyway and Severin will need someone by his side ruling the kingdom. (hide spoiler)]
Jalilah It said Jack's Faerie mother had cheated on The Alder King and gone with a human. This resulted in Jack, but it never says who the human was
Melissa After they hint that Jack's mom cheated on the King with a human and tried to hide him away, they then strongly imply Jack is the dead King's son and that his mom hopes Severin and the King kill each other so Jack can rule. Which Jack vetos. Much as I love this book, this is one of several sections that was not very well explained.
Lauren I thought they were hinting at the king or even severin, but I don't think that adds up? But yeah, I thought they were hinting at it too and I think I might have just missed it