Yes he is. In the series finale when Jack picks Jen up and puts him on his shoulder she mentions "the time that CJ knocked me up and left me". I do believe that was something that was said or pretty close to it at least.
no they never said who the father of Jen's baby is all they mention about the baby daddy is when Jack picked her up and she said "hey guys remember when my boy-friend knocked me up and left me to raise a kid on my own" the finale was 5 years into the future therefore the dad could've been any random guy.. If I recall I think C.J either died or moved to a different state I hope this helped..