Same: curriculum, academic goals, technical admissions standards, many day-to-day activities.

Different: teachers, vibe, guest speakers, special events. MakerSquare has a dev house, Hack Reactor doesn't. Hack Reactor has an alumni lounge, MakerSquare doesn't.

Applicants should apply at both places and go to whichever they personally connect with more. They're two top programs, academically and in terms of student outcomes (before and after the acquisition) so you can't really go wrong.