A case could easily be made for both of them.
It could be Booth, because he obviously is very protective of Brennan, plus he's got to have some residual feelings from his coma-dream (or whatever) and he would hide it because he's very respectful of the FBI and their rules, so he wouldn't want to admit romantic feelings for his partenr. And it COULDN'T be Brennan because she would probably not evne recognize whatever she felt as love, much less feel the need to hide it, much less be able to hide it.
Or, it could be Brennan, because of how she acted ever since she found out Booth was hallucinating Stewie and because Booth's likely the longest relationship she's ever had with a man (unless you count Hodgins, and I dont', for the purposes of this discussion). She would hide it because she's friends with Booth and she would probably not know how to tell him without ruining their friendship and partnership, and because it's just not rational to let personal feelings interfere with work. It COULDN'T be Booth because if he felt something for her, he'd just say it, at least to Angela, or he'd be way more awkward about it, like he was during several episodes with Cam.
Okay, that's my rationalizations. Now, we just have to see if one of my slightly neurotic and obviously obsessive and much-considered arguments are correct!