Sadly, Billy and Tommy were never real in WandaVision
The two children in WandaVision are creations of Wanda's reality-altering magic, as is the Vision in that series. As such the WandaVision are not real 'children' have no 'father'.
So where did they come from?
What we learn in Dr Strange in the Multiverse of Madness is that Wanda's dreams of the children are actually reflections of real children of other variants of Wanda in other universes. The children of WandaVision are therefore the product of that subsconscious knowledge.
The movie avoids drawing any attention to the identity of the father
The variant of Wanda in the 838 universe actually really lives in WestView with her two real children. Their father never appears in the movie, is never mentioned, and provides no childcare when Wanda leaves them unattended having been possessed by the dreamwalking Scarlet Witch from our universe. There seem to be no family photographs at all in Wanda's house in WestView.
As Wanda actress Elizabeth Olsen explains:
“... there is this multiverse, and in the version of the universe this woman wasn't with Vision. We liked having that be a mystery. For some reason he's not in her world. I always thought of her as more of a domestic Wanda. They got divorced. They're separated. She's not wearing a wedding band for a reason. Like those kinds of things. We liked the idea of her being on her own. The idea really is that the most important thing once you become a mother in the world are your children, and that's why.”
Are the children magical creations or natural procreations?
Olsen's remarks tend to suggest that these children were naturally conceived with a human father, who is no longer on the scene.
There is precedent in the Marvel Comics for the children to be magical creations, but this would call into question the Scarlet Witch's overall strategy in Doctor Strange in the Multiverse of Madness. If the creation of magical children is possible anywhere in the MCU multiverse, why doesn't the Scarlet Witch use her collosal magical powers, the Darkhold, and her multiversal knowledge to do this, rather than stealing the children from another Wanda?