At the end of the finale it is pretty clear that he has fathered a child, something that cylons cannot do (easily). This rules out both him and Kali.
Hold on now your Assuming the Chief is the father. We have no definative confimation that he is. But I would Also assume so.
Back in season 1 as was stated by Sharon to Helo the cylon human models can not reproduce with one another because there is apparently no love they feel for one another. But if a cylon loves a human they can get pregnant. There was no mention that male cylons can not impregnate human females. The key to the cylons having children was LOVE.
So what i am saying is you cant discount either from the suspect list cause cylons do get pregnant if there is Love