I'm gonna go ahead and add DC to the mix. It has 3 airports, an excellent metro and bus system, Verizon FIOS, relatively cheap out in the exburbs or apartments in formerly sketchy neighborhoods, and great proximity to NYC.
The only issues are the lack of people and VCs. You can always do contract work for the government though!
Another point for DC. Don't forget it's a great place to start a business if you want a way in to have the gov't or DoD be a customer.
SBIR programs are available, which are almost free $$ (you dev a product they need, they'll help pay for its development, and then buy lots of them from you). $70k instead of millions, but they don't take any part of your company in return.
There are apartments by metro stations, but you also have ZipCars http://zipcar.com which you rent by the hour ($9.25/hr weekday in DC, $11/hr weekday in NYC).
I grew up in DC, and now live in NY. If you prefer a suburban life, go DC. If you like the city, NY. One benefit of both places to The Valley is the gender ratio here -- slightly biased for more single educated women than men. I've heard the valley's a sausage party. Although I've heard really good things about LA in this dept.
Another point for Boulder Colorado, some friends enjoyed the tech startup culture there, too.
DC is for the most part a soul sucking environment. I grew up there and I moved to NYC. One thing that I noticed was, a hacker attitude plays much better in NYC than DC. Being rude and abrupt is tolerated if not respected in NYC (I'm talking about general life, non hacker circles), in DC saying things honestly and decisively is not a valued trait.
The only issues are the lack of people and VCs. You can always do contract work for the government though!