Thanks for some of the feedback.
My plan is to pursue a PhD in Middle Eastern History after my MA, but with an eye to doing research/work on foreign policy (probably won't teach until later in my career if at all). My interest is therefore a mix of both history and policy. Positioning myself for a PhD program is a high concern, but I also want to make sure that my MA degree is marketable in the policy world. My perception is that Georgetown's program has a great mix of language, a contemporary policy focus, and a good grounding in Arab history. I think an SFS degree would certainly help in future work in the policy world. On the other hand, Harvard's program allows you to draft your own curriculum and certainly carries weight in terms of PhD preparation, and the options to tailor the curriculum to my interests is nice. My main concern with Harvard is that the AM program does not really have a strong departmental home. All of the courses are outsourced to other departments, and I'm a bit worried that the attention paid to MA students will suffer as a result.
I guess my most important questions are a) will the MA degree from Harvard carry as much weight in the policy world as the MA degree from Gtown's SFS Arab studies and which school offers me a better chance of gaining admissions to a top PhD program.