Hey Joshua,
I'm currently in the throws of a development project in Brooklyn, and the $300 a sf model is a little light, especially if you plan on decent finishes. You are correct, that this has long been the conventional figure used to estimate cost for buildable sf in NYC. Also, I'm not sure if you are demoing an existing structure, if the structure is freestanding, etc, but this will obviously greatly affect your overall budget.
For our project, most of the material prices are in line with expectations, but where we've been shocked with recent increases is the soft cost. Our insurance policy for the project alone was well over $100k. Lawyers, engineer, architect, expeditor, surveyors, etc pile on the fees quickly. We also had to negotiate access agreements with both adjoining neighbors, which added nearly another $100k.
Best of luck in your venture, feel free to contact me directly with any questions or if you would like me to pass along any of my resources.