Don't let the current 'rebuilding' of NT at Notre Dame put you off from applying. Both Fitzgerald and Lincicum will take students, and in the next two years two more NT faculty will be added (to account for Moss's departure and D'Angelo's retirement). At the same time, the early Christianity faculty is very strong (top in the country), and plenty of opportunities to study with Classics faculty.
I should add that I am a current CJA PhD student, and, to @Onthenahar, if you are interested in 2nd and 3rd century, CJA is probably a better fit. If what you are interested in is history of doctrine, then HC might be better; but for anything else (social history, history of biblical interpretation, etc.) CJA likely makes more sense.