Besides the cities themselves being quite different, there are no major differences between taking the course in SF or NYC. We closely track assessment scores across campuses, and have found student performance to be consistently comparable across SF and NYC. The NYC campus has on average 60 students per class while SF has around 80. Regardless of class size, App Academy ensures that students will have the opportunity to speak with instructors as often as needed. Both campuses keep about an 8:1 student:teacher ratio. App Academy HQ is in San Francisco.
For more information, read this Quora post.