Its difficult to answer your question without more detail into what you're looking for. Are you simply looking for a great city with an amazing program (San Francisco)? Or a city with a strong environment of training programs (New York or Boston)? In answer to the later, as in "which major citites have the largest collection of top or excellent neurology residencies?":
I'd say a toss up between NY and Boston. Although Boston has Partners, I would give the edge to NY having 4-5 excellent neurology residencies.
New York (Columbia, Mount Sinai Icahn, NYU, Cornell, Montefiore)
Boston (Partners, BIDMC, Tufts, BU)
LA (UCLA, USC, Kaiser, Cedars)
Philadelphia (UPenn, Jeff, Drex, Temple)
SF (UCSF)
Cleveland (CCF, Case)
Chicago (Rush, U Chicago, Northwestern)
Houston (UT Houston, Baylor)
Atlanta (Emory)
Miami (U Miami)
Seattle (U Wash)
Dallas (UTSW)
That's really as far as I can go before just breaking down into a top program list (Ann Arbor, Baltimore, Rochester...)