I am a bit of an NYC snob myself, as I usually spend my summers there. You can find decent pizza at almost every corner.
However, I have a deep appreciation for Applewood's in Menlo Park CA. It is a different kind of pizza, like none I have ever encountered (I think the crispy-chewy crust is key to its elusiveness). Absolutely amazing, if you live on the peninsula it is worth the trip - plus they have an amazing selection of great German beers. You might run into me there on my weekly trip with my buddies!