Whether or not Swift himself was a misanthrope is a question for a historian; Swift's novel, Gulliver's Travels, however, certainly expresses a misanthropic view.
Many of the peoples he discovers in his travels are intended as parodies of human weaknesses.
In Lagado, for example, Gulliver visits the Academy, where he mets "scientists" working on projects such as "extracting Sun-Beams out of Cucumbers," and reducing "human Excrement to its original Food." Another researcher is involved in a scheme to abolish the use of words, since "every Word we speak is in some Degree a Diminution of our Lungs by Corrosion." All of this is a parody, of course, on the obscurantism of some scholars.
The most misanthopic section of Gulliver's Travels is Part IV: A Voyage to the Country of the Houyhnhnms. The Houyhnhnms are a race of intelligent, clean, talking horses. Their behavior is "orderly and rational...and judicious." Their morality is so pure that their language does not have a word for lying.
The Houhynhnms share their land with a creature known as the Yahoos. They are human-like, but stupid, brutal, and filthy. The Houhyhnmns use the Yahoos as slaves.
Gulliver realizes that he is not much better than the Yahoos, and he becomes ashamed of his humanness. When he finally returns to England, he is greeted by his wife and children, but is repulsed by their similarity to the Yahoos:
The Sight of them filled me only with Hatred, Disgust and Contempt...My Wife took me in her Arms, and kissed me; at which, having not been used to the Touch of that odious Animal for so many Years, I fell in a Swoon for almost an Hour.