Given that the religious aspect might be sticky, just remember that Canisius does not have an obviously Catholic/religious name, and is too small and regional for many people to know much about it. Thus, people are not likely to wonder about his religion with a Canisius degree. St. Bonaventure has the word “saint” front and center in the name. For the rest of his life, he will be asked if he is Catholic when people hear where he earned his degree. With Canisius, people will just want to know where it is.
As others have pointed out, the Jesuits are the foremost educators (and scholars) in Catholicism and Canisius is Jesuit while SB is Franciscan.