the second bit is more formal, " You're six years old, aren't you?"
because, the other sounds very demanding or imperative, like as if you have to answer the question. so, it has to be the second line.
Answer:
Father Flynn argues that Sister Aloysius has been “out to get him” for a long time. In an effort to defend his innocence, the priest mentions that Sister James believes that the accusations are false. Father Flynn grows increasingly aggravated, and he demands that Sister Aloysius provide him with concrete evidence that supports the allegations brought against him. After she replies that she saw the priest grab another student’s wrist, Father Flynn responds that he will have Sister Aloysius removed from her position at the school.
Proctor believes Parris is only in it for profits and he believes he that he is not worth his time listening to Reverend Parris Preaching.