For pizza I usually go by the slice, (eg. some pizza places have one or two type of slices that are the best, and the rest might be ok). I almost never go at sit down pizzeria. Usually the "by the slice" places are better than sit down restaurants (which usually cater to tourists).

My favorite slice by far is the marinara and sausage/meatball (the pizza on the background):

https://lh5.googleusercontent.com/p/AF1QipP3K30cRMfe41WljFJP...

The place is called "Stromboli Pizza" and is in the middle of East Village. When the weather is great is just grab a slice and sit down at the stools outside "The Bean", which is next door on 9th st.

http://www.strombolipizzanewyork.com/menu.aspx

If you want good Italian in NYC go to Celeste, owner is actually Italian too