Which has a better archaeological program Harvard or Brown?

It's going to be your preference. Both institutions have the preferred regional accreditation. Therefore, the coursework and degree you complete through either school will be recognized by all other colleges and universities as well as employers. Look at the admissions requirements, tuition, majors, environment, student services, professor to student ratio, classroom size, student activities etc. Then choose the one you feel will meet your needs best. Both institutions are excellent, so you can't go wrong with either.