Hey congrats on the two Masters acceptances - that's great news
Which doctoral program you choose I think is really guided by what your specific interests are - both schools are exceptional and highly regarded for their teaching, research and activities in the global health field. The two have different doctoral tracks (except for Health Systems) and you may find slightly different core interests. Harvard also seems more invovled with economics, but that's due to the leading faculty they have in that area.
I agree re: Baltimore - it's another factor to consider, though there are nice parts of the city it isn't the same as Boston for sure. Perhaps a testament to JH strength that they attract such great scholars there despite the location!
Healthfourall - yeah I applied to both those programs too! I see someone got their rejection today, hopefully the decisions for the rest of us not too far away. I am not sure which is stronger in this track - and I think it all comes down to personal goals again. For instance, Harvard has a more interdisciplinary approach with other graduate schools, ethics faculty, politics etc in their course (all of which attract me), but Johns Hopkins has a strong child health focus to their department (which is another interest of mine) and maintains a good breadth to the systems curriculum.
One member of the harvard faculty I contacted said that the global health focus of the school is likely to increase over the next few years as Julio Frenk is keen on this.
Hope that helps - let me know when the decisions roll in!