I would say there are several potential candidates. First, as the answer previous to this one has already given, there is Skyris Bolgolam, who certainly emerges as a major candidate, given his longstanding enmity against Gulliver, as well as his role in originating the proceedings against Gulliver himself. However, I would suggest adding two more potential choices, who one might also make an argument for being Gulliver's most dangerous enemy.
The first is the Empress herself. This is because of the manner of her humiliation at Gulliver's hands, during the fire, for which she feels lasting animosity towards Gulliver herself. Hers is a very deep, very personal kind of hatred, which makes her a very dangerous threat behind the scenes. Indeed, Bolgolam himself is referred to at one point as "a creature of the Empress" (Swift, Gulliver's Travels, chapter 7).
The second option is actually the Emperor of Lilliput himself. After all, he is, first of all, the most powerful person within Lilliput, and secondly, it's important to note that his relationship with Gulliver can be a problematic one. The key scene here emerges in chapter 5, when Gulliver destroys Blefuscu's fleet, and the Emperor voices his desire to utilize Gulliver against his rival nation, to reduce them to a subject nation. Gulliver refuses to submit to the Emperor's plans, something for which Gulliver himself notes the Emperor "could never forgive" him (Swift, Gulliver's Travels, chapter 5). Theirs is a somewhat problematic relationship because although Gulliver does rise within the Emperor's favor, he falls from it as well. And this is an important factor, considering the very real power that the Emperor wields.