If you have both the time and the money, applying to more schools can only help you, as you'll have more opportunities to obtain an acceptance. With regards to your geographical concerns, however, what you should ask yourself is if you'd be willing to go through the application cycle again just to matriculate in either CA or NY. Basically, would you refuse to go to medical school anywhere else, even if offered a spot outside of CA/NY? Unless you can say yes without a shred of doubt, I would highly recommend that you add additional schools to your list. Keep them within the vicinity of your desired area if you wish (for example, some PA schools are within easy reach of NYC), but ultimately make sure that they are a good fit for your statistics.
Also, do not be so hard on yourself! That undergraduate GPA for an engineering/physics double major is respectable, and your overall MCAT score is in the top 10%. You are certainly a competitive applicant, especially with your EC's. Do not let SDN's biased/self-selected population make you think otherwise; it is NOT indicative of the overall applicant pool!