Zoey spends the majority of season two with Luca, so if she is pregnant, he is most likely the father. But, as we see toward the end, they are super unhappy, which doesn't really bode well for a romantic relationship when they can't even look at each other without getting upset. We can also assume she and Aaron are spending a little bit of time together during the Summer, whether he goes to Paris to visit her, or maybe when she flies home.
But when it comes to Zoey's track record of indecision, it is safe to guess she more likely than not is hiding in her work instead of spending any time with the guys in her life.