I'm probably going to ruffle a few feathers here, but here's my thoughts.
Skip DiFaras. The toppings are great but the crust is mediocre- the only thing you're getting is ambiance and you can get that elsewhere, without having to stand in line for hours. DiFaras is pizza theater, not great pizza.
Do you really need to go to four coal joints? Just do Patsy's in Harlem or Lombardi's.
You need a slice place. Right now, there is no truly great slice place in NY. Joes is famous, but the reviews are a bit mixed. That's pretty much all you've got, though, so that's where I'd go.
Is this a NY style only tour? What about Neapolitan? Keste or maybe Motorino would be worth a visit.
Co. is a bit hard to classify, but I've heard great things about it and I have tremendous respect for Jim Lahey.
How are you getting around? Car? Subway? If you've got the transportation, I'd go up to Johnny's in Mount Vernon. Out of all the New York style pizzerias in the metro area, Johnny's is the only one I have any interest in visiting.