Corey makes his statement against Hathorne as a judge to make clear that the court in Salem is not concerned with evidence. Corey makes his presence known in Act III with the resounding call that seems to reverberate and haunt the courtroom simultaneously: "I have evidence for the court." When Hathorne emerges to criticize Corey, Giles responds with the idea that Hathorne is not fit to be a judge. The reference to not being a "Boston judge yet" helps to enhance this. In making such a statement, Corey is able to bring out reasonable doubt in terms of the people in the position of power in the witch trials. This element will be reinforced with how Hale and Proctor criticize the court later on in the sequence of events.
Corey's statement about the qualifications of Hathorne is a way to suggest that he, himself, has the legal capacity to question both the evidence being presented against his wife and offer evidence to counter it. When Hathorne asks which lawyer prepared his deposition, Corey's response suggests that he is of a legal caliber equal to those who sit in judgment over citizens of Salem. Giles's statement is to make clear that those in the position of power might not be worthy of their titles. In making this comment early on in the act, it becomes clear that the legal standing and legitimacy of the court is brought into question.