What is a counterargument in Animal Farm that Napoleon was not in charge?
This is a difficult argument to make. For the duration of the story, especially at the end, Napoleon was in charge. No one came close. When there was an attempted rebellion, he destroyed it with a massive massacre. In light of this point, the only way that we can argue that Napoleon was not in charge is the end of the story, when he became a man.
That he became a man shows that he is still striving to become human. Hence, he is still subject to the worldview of men, not animals. Hence, we can argue that within his categories of thought, he still is shaped by the human world. So, if anyone is in charge, it is the human world. Admittedly, this line of reasoning is more philosophical and sociological.