Bois-Guilbert is the obvious choice for Ivanhoe's main villain. He is snotty, hates Saxons, helps De Bracy kidnap Rowena, kidnaps Rebecca himself, and basically causes a lot of trouble. Even his face looks cruel and proud. Everything about him screams, "I am evil!" Give this man a fluffy white cat and an armchair and he could be the bad guy from an old James Bond movie.
Beaumanoir only appears in the last ten chapters, but he makes those chapters count. Beaumanoir is everything a stereotypical medieval judge should be: prejudiced, arrogant, and self-righteous. It never occurs to him that Rebecca might be innocent of the crime of witchcraft. The only thing Beaumanoir has going for him, morally speaking, is that he disapproves of all the luxury and wealth that the Knights Templar have accumulated in their battles in the Middle East. He takes the Templars' vow of poverty seriously and does his best to make his men live according to the principles of the Order. He's not a hypocrite like his little helper Albert de Malvoisin. Still, Beaumanoir listens to Malvoisin, which points out his bad judgment.
Prince John is a real-life antagonist to King Richard, since he did rebel against his brother and ultimately became king after Richard's death in 1199. We don't really see much of him in Ivanhoe; he is more a force of badness working in the background. He plays a much larger role as the antagonist in a lot of traditional tales of Robin Hood – for example, in the 2010 movie Robin Hood, starring a somewhat tired-looking Russell Crowe.