2nd Santarpios!!! Real deal

You can walk to Regina's in the North End from your hotel in the Seaport area. Numerous excellent Italian restaurants and pastry shops in that neighborhood. Enjoy.

I am not a fan of Pepe's Pizza . NYC pizza is better

I'm a native NYer and grew up on NY 'za. Lots of good options there! When I moved to Boston, people told me to go to Regina's. I went to their location in the old Haymarket which doesn't exist anymore. Meh. I wasn't impressed. (I had a college friend who grew up on Thacher St. in the North End, spitting distance from where the original Regina's was and still is.) Now, Regina's is a chain or franchise or something. When I was a student , I'd sometimes head to Haymarket for food shopping on Saturdays but I'd cross over to Hanover St. in the North End for pizza. My favorite place had a storefront that opened up entirely (in good weather); from google maps, it might have been Cafe Paradiso or whatever that location used to be called. It was usually old Italian guys speaking Italian and drinking espresso (or something stronger) and me. I preferred their Sicilian style (made in a large rectangular baking pan). It was pre-yuppie, local, not touristy, and reasonably priced.
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On trips back and forth between NY and Boston, I would sometimes stop in New Haven. The first time I went to check out Pepe's, the line was at least 3 hours long. No thanks. So I went to Sally's a few stores over, with a shorter wait time. Sally is Sal for Salvatore. http://en.wikipedia.org/wiki/Sally%27s_Apizza (Like Sally in Cindy Lauper's "Sally's Pigeons." http://www.youtube.com/watch?v=KxwDnypJw3Y Sally is Salvatore; "Sally let HIS pigeons out to fly." and the official video shows a guy, Sal = Sally, letting HIS pigeons out to fly. Her friend with the pirate smile is NOT Sally of the title.)  
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On another detour to New Haven, I made it to Pepe's. It was the most I ever paid for a pizza up to that time. The most distinctive thing I remember is that it was (deliberately) not a neat circle. It was a crooked, uneven shape as if to prove it was hand made or hand tossed and unevenly baked: some blackened char and some "normal" unburned parts. I think that Sally's and Pepe's probably brag about their homemade ingredients (home made sauce, not from a can or a 55 gallon drum; home made sausage; home made dough; cheese? do they make their own cheese? I don't remember.) but I'm not enough of an expert to tell the difference between good home made and good canned. I CAN tell the diff between good home made and bad home made or good (one) and bad (the other). Anyway, Pepe's and Sally's were both OK to good but not worth the long waits. And now Pepe's is a chain extended to Boston but I have yet to visit the one near me.  
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I don't remember my old haunts in the NY neighborhoods I lived in or bicycled to or subwayed to. They were small, privately owned, single location places with names like "Vinnie's" or "Sal's" or "Palermo Pizza" or "Napoli Pizza" that probably don't exist anymore. These days, I only visit central Manhattan or other neighborhoods where friends and relatives live that I didn't go to for 'za as a kid. These days, most of the NY places I stop in for 'za are OK to good but they lack the nostalgic enhancement.  
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In Boston, I used to like Pizzeria Uno (the Chicago based chain). It was fast, reliable, consistent, had plenty of toppings and tasted good to me. I haven't been to Uno's since before Covid so I don't know if they're holding up.