I've been going through a pizza phase lately, which I am happy about. Let me list some places I've been to recently, in no particular order...
1) Veloce Very good "grandma style" pie. Square but not extremely thick.
2) Motorino Went to the new East Village branch of the East Williamsburg pizzeria last night. As described in the Slice write-up, there was indeed a bit of char on the crust, but not much, and overall it was a great pie.
3) Saraghina If you can make it to Saraghina alive, you have quite a treat in store. A very cool place (in a somewhat "sketchy" neighborhood).
4) Adrienne's Went there a couple of weeks ago when my aunt and uncle were in town, and will be going there tonight.
5) Sally's Went all the way to New Haven (90 minute trip on Metro North) for pizza a few weeks ago and it's completely worth it.