Again, congratulations to you. Great options, both of them. I would think the differences between Cornell and Yale's academic reputation are negligible. Match list differences are negligible as well. Both schools are sending their graduates to their top 1 or 2 choices. You couldn't make a mistake choosing either of them from that perspective.
Cornell has a decent primary care clerkship and a small public health department that makes the most of its location in New York. However, it doesn't seem that primary care in Manhattan med schools is all that emphasized, mostly because primary care doesn't really exist in any traditional form in New York City. Maybe neither school is all that strong in primary care.
Both schools will probably make certain that you see all kinds of patients during your third and fourth years. Cornell rotates through hospitals all over the 5 boroughs. I would expect Yale students see about as much as New Haven has to offer, and as I recall there is some ethnic diversity there.
As mentioned, the Macys Scholar program exists for those who want dual degrees. Cornell also has a new MD-MBA these days for those interested. I know one thing that makes Cornell stand out from its peer schools is the international program. More than half of all fourth years travel on funded international projects, and a sizeable number of first year students as well. Though perhaps Yale has opportunities as well.
In the end, it may come down to location. New Haven isn't all that bad, but it isn't all that great either.