NY tends to be a strong presence in almost everything. As a port city and major economic and cultural center, it has great diversity in culture, not to mention that it is one the places in the country that people move to specifically to 'make it big' in their endeavors, including martial arts. With a strong international community, it is ideal for the martial arts.
Washington DC is, to a lesser extent as well, and for many of the same reasons. Having lived in the DC area all my life, I can say that if there is a martial art, there is likely a school for it somewhere if you dig hard enough. Jhoon Rhee's presence here doesn't hurt either.
SF I'm sure is similarly a hot spot, though it has been over two decades since I've been there, and at that time, it was not for checking out dojos. I remember the city very fondly, particularly how nice the climate was as compared to the DC area.
Daniel
Yeah, I did a search of NYC schools on the internet and was very impressed by what I saw. I would love to go to John Perkins school.