Now, just because Buffy doesn't know the father's identity doesn't mean that the creators of the book don't know. In fact, it'd seem pretty unlikely that they'd make a move like this without knowing exactly how it happened in-universe and where it's going. It also doesn't prevent us from speculating, which is what I'm about to do here.
First, while Dark Horse hasn't officially confirmed it (at least that I've seen), they've certainly leaned in the direction that Buffy got pregnant at the party seen in Issue #1. Putting aside how problematic that timeline is, that means we can eliminate a number of potential fathers. It's not Angel (or Twilight) and it's not any random person Buffy would have hooked up with in San Francisco between Issues #39 and #40 of Season 8. So we can narrow our candidates list to the males who appeared at the party at the start of Season 9.
So who are they?
Well, by my count, there are seven potential candidates from the party, not including the two police officers and other random unnamed partygoers. Rather than try and rank the likelihood of each candidate over the next, let's just take a look at each of them in alphabetical order.
Andrew's sexual preference has never been officially clarified within the Buffyverse, but judging from Buffy's greeting to him at the party, it's pretty clear SHE thinks he's gay. Now, if both of them got black-out drunk, it's not out of the question, but it's highly unlikely he's the father.
Coffee Shop Boss
When Buffy arrived at work the day after the party, her boss sent her home, saying, "I told you last night not to come in. You know, after..." What "after" meant is left unsaid, but it's entirely possible they hooked up. Still, given that they haven't even named this guy yet, I'm not putting my money on him.
The morning after the party, Buffy receives flowers from her new neighbor in apartment 2D, a man who signed the card "Heinrich." Most of the speculation about Buffy's pregnancy has centered around this mystery man, and I wouldn't be surprised if he turned out to be the father. What WOULD surprise me is if "Heinrich from 2D" is actually just some random guy named Heinrich. Hell, "Heinrich" could be any of the six other guys on this list, or even someone else from Buffy's past.
Riley is a male. Riley was at the party. Riley and Buffy have a sexual history. Those are the reasons why Riley COULD be the father. The reasons not? Well, literally everything else, most notably that Buffy, in only the early stages of drunkenness, seemed put off by the fact she was even flirting with the married Riley, so I can't imagine she would have taken it much further.
Spike was also at the party, and Spike and Buffy also have a sexual history. But I don't think Spike is the father, mostly because, well, he's a vampire. In the course of canonical Buffyverse works, there's one instance of a vampire being able to impregnate a woman. However, Darla's pregnancy by Angel wasn't natural in any way. Connor's conception was a gift from The Powers That Be, fulfilling the life that was owed to Angel after he completed The Trials for Darla. Angel was never able to impregnate anyone else throughout the course of the series, and I don't think Spike would be able to either, especially not after the destruction of The Seed.
Buffy's strangely named roommate was grilled by Dawn about the origin of his name, but one possiblity she didn't guess was "a good Tumble in the sack", which is maybe something he had with Buffy. Then again, he hasn't brought it up since (if it did happen), and he was fully ready to kick Buffy out of the apartment in Issue #5, so he doesn't seem like daddy material.
And now we come to Mr. Harris. There's a scene in Issue #1 that hints STRONGLY that something happened between Buffy and Xander. Something Xander didn't want to talk about and Dawn never has to know about. But what if that something was sex with Buffy, and what if the guilt got to Xander, to the point that he told Dawn. Wouldn't that go a long way toward explaining why Xander's been in the doghouse since that issue, and why Dawn hasn't exactly been welcoming to her sister? Xander being the father of Buffy's child would be a complete MESS for the Scooby Gang, but dramatic gold for the series as a whole.
Of course, given that Buffy doesn't know the identity of the father, it's unlikely we're going to find out any time soon. Still, it could be fun to go on this journey with Buffy, as she transitions from being a Slayer to a mother.