But Kant didn't say that we could only perceive three dimensions. Kant said that there WERE only three dimensions. He was directly saying that the existence of four or more dimensions was absolutely impossible. Kant made specific statements about the actual structure of the universe which have been proven false.
Anyhow, there are two refutations to the perceiving three dimensions issue.
1) Many mathematicians, who spend a long time working with four (and higher) dimensional objects, actually do develop the ability to perceive them in the same way that people normally perceive three dimensonal ones.
2) Physics experiments are perception, that's why we do them.