There are various candidates for smartest animal on the farm, all of them pigs. The selection among the pigs really depends on one's definition of "smart."
Old Major is the visionary, the one who has worked out for himself the nature of the animals' existence and the forces that shape their lives. Although he is only present at the beginning of the book, his is probably the most powerful and insightful intellect.
Snowball is the most inventive and brilliant of the pigs. He is smart in the sense of being an ideas man, as well as, like Old Major, a utopian intellectual.
Napoleon has the most practical mind among the pigs. We might describe his variety of intelligence as "street smarts." While he lacks Old Major's breadth of vision and Snowball's theoretical brilliance, he is able to defeat his enemies by being more strategically-minded.
Squealer is an example of the type of intelligence which allies itself with power and provides legitimacy, while receiving numerous privileges. Unlike Napoleon and Snowball, Squealer is not a leader but is able to manipulate others into doing what he wants.
If one were to attempt to measure their intelligence by some method like an IQ test, I believe Snowball would score the highest of these four pigs and Napoleon the lowest. Conversely, if you measure "smartness" by practical success, Napoleon would top the table and Snowball would come last.