I've heard this from friends, teachers, and professors, but never really seen any evidence aside from the fact that some portraits look similar side by side. Are there any well supported theories that prove or disprove this?
The answer here is no. Even a simple image search for depictions of Jesus shows images with blond hair and blue eyes well before the life of Cesar Borgia. While that does not mean that Cesar Borgia's likeness was not used as a basis for Jesus' images, just that he was certainly not the inspiration for the blond haired blue eyed architype.