For NY style, I haven't found anything able to beat Tony's - Ballantyne. IMHO, if Tony's is a 9.9 (leaving room for improvement), some (but not all) notables are:
Hawthorne's (Elizabeth) - 9.5, good enough that if I lived uptown I likely would not drive to Tony's. Tried Carmel Rd location but for some reason didn't seem as good.
Mario's (Matthews) - 9.0 Naturally similar to Tony's as I guess you could call them 'affiliates' since Tony and Mario grew up together - see for yourself
http://www.tonyspizza.org/ http://www.mariospizza.org/
Portofino's (southpark) - 9.0, but for me, it's difficult not to get their linguine/clams ....although it's been a few years since I've had it.
Lorenzo's (ardrey kell/marvin)- 9.2 Very good, but I suspected the sauce to be less tasty than Tony's. I brought a side of sauce to my table and sure enough, everyone at the table agreed. But again, it's very good.
plan to try: Luigi's