Hmm. Problem is many of my favorite less known Manhattan places have closed as rents increase, and you don't need me to tell you to go to John's.
The Famiglia local chain that Seth noted is pretty good. There used to be one near my office and it closed. Despite being a chain they do vary so if he recommends one try there.
For something oddly unique venture uptown to my old haunts in Morningside Heights and go to Koronet Pizza. Largest slices you've ever seen. In fact, start typing "koronet" into google and look for the autofill. Despite the seeming novelty of the size, the pizza is also quite good. In my student days the jumbo slice was $1, and only $1.75 to be loaded with pepperoni. It was enough for dinner. Best student meal value in the city. Prices are higher but it's still a deal today.
http://slice.seriouseats.com/archiv...izza-slices-morningside-heights-columbia.html
Just don't fold the slice when you eat it. Due to the size everything ends up sliding down into the well, especially toppings. Damn physics.
Rosa's is another mini-chain. It has a few locations that I know of in Queens plus one near MSG in Manhattan. Quality stuff with very good Grandma's slices.
I would be remiss if I didn't mention Drainyoo 's family has a joint in Astoria. Dino's at 30-01 Broadway.
Finally, I'm not sure if Pirlo is too cool to venture even further into Queens. There are more than 3 dozen pizza joints within a 2 mile radius of my house. I made a little photo project out of it. Highlights include the aforementioned Rosa's, Carlo's, Phillie's and Gino's.
