I recommend Arturos in Manhattan on Houston(with Joe's still having the best by the slice in said borough, runner up being Pizza Suprema near Penn Station). Best in the outer boroughs is Catania near St. Barnabas Hospital in da Bronx, with Mike's on Morris Park being pretty good as well. In Brooklyn, I still love Gino's in Bay Ridge, with Elegante (in a now heavily Arab neighborhood) giving the best square slice. Rizzo's on Steinway is still good over in Queens, but stick to the squares.
DiFara's is OK, but Domenick has been wearing down due to popularity over on Avenue J. DAMN YOU Timeout NY!
These days you've got to go to Staten Island, Nassau or Suffolk for the good old thin crust no nonsense pizza. There are a few places in Queens that'll make you happy. The ones I know are along Union Tpke and Northern Blvd east of Springfield.
Two great places just across the line in New Hyde Park, Umbertos on Jericho and Iavarone's on Union Tpke.
There are probably dozens around but don't look for them in Manhattan.
Out where I am (NE Queens - NW Nassau) most of the good German delis have been bought by Koreans. They're smart though and keep the original owners on for a year to teach them how to get it right.
There's one strip by me that's got a dry cleaner, liquor store, green grocer, nail place, deli and pizza place. All Korean except the pizza which still has a guy named Sal on the oven.
Near the draft board on Jackson St.