Both programs are so similar that imo it's all up to personal preference. I think NYU is a bit more expensive, especially because it is hard to escape the high rent of NYC whereas in Boston you can move a bit out of the main city and pay a more decent rent and still be able to public transit or drive in. Despite NYU's higher research ranking, imo your research options at either school are excellent and equivalent, also if you really want to go hardcore research you can work with PI's at HMS, BI, Brigham, etc if you're in Boston. Check out match lists to see if you can see any big difference, last I looked at the two schools they both match plenty of students to excellent programs all across the US (including competitive areas like California/NYC/Boston).
IIRC NYU takes 3rd year boards, I haven't done step 1, but knowing plenty of people who went through 3rd year, I have no idea how people could have the time or energy to study adequately for boards. Or how easy it is to refresh all that knowledge from 2nd year after so long away from the books. But that is a question you should ask some rising 4th years or recent grads of NYU, or at least some rising 4th years+ at other schools on what they think about it. That was one of my only big concerns about NYU's curriculum.
In short, congrats on two excellent schools. If you can't find one you like more than the other, go ahead and choose where you want to spend your next 4 years more.