Yeah, all of them. Every single one—including Dog Man and M'ling—are the antagonists of the novel.
Now, we should point out an important distinction here. An antagonist and a villain are not the same thing. A villain is a bad guy, a morally corrupt individual with a maniacal laugh and probably a secret lair hidden in a volcano or Starbucks. An antagonist is the character—in this case, characters (plural)—who creates obstacles the protagonist must overcome. He can do this out of pure, evil spite, but sometimes the antagonist can be an antagonist simply by existing.
The Beast Folk are mostly the latter, and the obstacles they present Prendick vary from creature to creature. On the one hand, Hyena-Swine becomes an obstacle of survival for Prendick. On the other hand, Satyr and Ape Man openly question Prendick's status in the island society, causing problems when Prendick needs to replace Moreau as the one in charge.
Still other obstacles are internal for Prendick. For example, Prendick has an inner conflict with regards to the Beast Folk as he both hates and pities the creatures. This is particularly true during the hunting of the Leopard Man.
We'd like to add a quick side note before we move on. In the "Symbols, Imagery, Allegory" section, we discuss that the idea that Moreau's island symbolizes civilization. If that's true, then the Beast Folk represent various classes of people within society, meaning the ultimate antagonist of The Island of Dr. Moreau could be society itself. Did you hear that squishy sound? That's the sound of someone's mind being blown.
Did we throw you by mentioning the Beast Folk first? Well, Moreau isn't a straightforward antagonist. Sure, he's responsible for the whole messed up situation and he's not exactly a good guy, slicing up animals like does, but he's not actually out to get Prendick. If it were up to him, Prendick wouldn't have crashed his vivisectionist party… To an extent Moreau's and Prendick's interests actually line up—they're both men of science—but Moreau takes it to such a nut-job extreme that Prendick can't help but reject Moreau's views.
Moreau the person is less of an antagonist than Moreau the worldview. Prendick is horrified when he realizes that he's attracted to the perks of this worldview—heck, who doesn't want to save time by not troubling with ethical questions.
Yet had I known such pain was in the next room, and had it been dumb, I believe—I have thought since—I could have stood it well enough. It is when suffering finds a voice and sets our nerves quivering that this pity comes troubling us. (8.26)
It's the fight against this antagonistic feature of Moreau—Moreau's ideas—that is a central struggle for our protagonist Prendick.