There's NO WAY Claire is the mother of Sylar's kid. The writers can get weird, but not THAT squicky. No, the mom was no one in that household confrontation since there was no recognition to that effect from anyone. And since we've seen Tracy ended up with Nathan, that rules her out, too. Which leaves two candidates around Sylar's age that I can think of: Maya and Elle.
My money's on Elle. I seriously doubt Maya would go near him again since he killed her brother and manipulated/deceived her for an entire season. Elle on the other hand, while Sylar did kill her father, is totally screwed up enough and desperate to be loved/accepted to overlook that little detail. Plus, I do think she harbors A LOT of resentment toward her father (for very good reasons) that hasn't come to the surface yet, so she may even come to feel that Sylar did her a favor. She already looks up to Noah, too (he may even be her new father figure), so I could totally see her wanting to name their kid after him, as well.