The short answer to your question is yes, the pigs are still running the farm at the end of Animal Farm by George Orwell; however, by the time we reach the final chapter of the novella, the pigs have undergone a change and are really no longer pigs.
Of course the story begins on Manor Farm, and the takeover by the animals is rather unplanned and therefore all the animals are relatively equal. It does not take long, however, before the pigs begin to assert themselves and take some extra benefits which they claim are necessary. Within hours of the takeover, the pigs have claimed all the milk and apples for themselves, setting up their eventual despotic rule of the farm.
The pigs are smart, no doubt about that. They are smart enough to keep all the good stuff for themselves and to get out of any physical labor--all without raising much in the way of suspicion among the rest of the animals. Napoleon manages to get rid of his only challenger, fellow pig Snowball, and it is smooth sailing from there for him and all of the other pigs on the farm.
Eventually Orwell makes it clear that the pigs are doing exactly the same things that Mr. Jones used to do. They are consuming without producing and they are treating all the other animals on the farm as if they were worthless slaves, good for nothing but what they can produce. The best evidence of this, of course, is Boxer. Once he is too broken to be of any service to the farm and especially to the pigs, they sell him off to the knacker to be killed and ground into dog food.
The pigs live in the farmhouse and act in nearly every way like humans. They dress in the Jones's clothes, they educate their children, and they do business with the humans in town and on neighboring farms. In the novel, the pigs never leave the farm, nor do they lose control of the farm to anyone else. The reason you ask the question, I assume, comes from the final scene of the novella in which the animals see something odd.
Napoleon has invited men to the farm (which has reverted back to its original name, Manor Farm) and he amazes everyone by walking on his hind legs--just like a human does. As they all sit around a table and talk, humans and pigs, the other animals look into the window and see something astonishing:
The creatures outside looked from pig to man, and from man to pig, and from pig to man again; but already it was impossible to say which was which.
Clearly the pigs have not given up control of the farm to the humans, but they have become so much like them that the animals can hardly tell the pigs from the humans. The pigs are in control, and they are just as oppressive to the animals as Mr. Jones ever was to them.
For more interesting insights and excellent information on George Orwell and his writings, try the eNotes links below.