My inclination is to say something deliberately controversial about how punk came from NYC and so New York street food is inevitably linked to the now-national punk culture, but that seems unnecessarily childish.
So I asked my girlfriend, who is a brilliant scholar, what she thought, and she mentioned two things: 1. Pizza spread nationally as a food through drive-in movie theaters in the '50s and '60s, so it's linked in our cultural consciousness to an adolescent sense of burgeoning independence. Punk as a subculture (rather than punk as COUNTERculture, which is different) highly values youth and is about creating a state of protracted adolescence, trying to maintain that juvenile sense of independence. Look at the facile anti-authoritarianism of Sum 41 or the newest Rancid record. It's a politic that isn't directed at anything tangible and doesn't propose solutions, that essentially, when you distill it, comes down to a refrain of "NO PARENTS." In fact, there was a fairly prolific vandal in North Brooklyn about ten years ago whose tag was a slice of pizza with the words NO PARENTS written above it.
2. Pizza by the pie, as opposed to pizza by the slice, is an inherently communal food. It's made for sharing; it brings to mind times of celebration, specifically birthday parties. I don't think it's a coincidence that I wrote a zine when I was 20 called Every Day Is My Birthday, or that the same phrase is the first line of the Hickey song "40 oz Of Bad Karma." Again, it's about fostering an atmosphere of constant partying. Punk may have its roots in the city, but it came to prominence in the suburbs, and pizza also evokes a sense of [urbanness] that inscribes authenticity onto otherwise banal suburban rebellion.
In short: Pizza is delicious, everyone loves pizza, even punks who hate everything.