I agree with everything in this tread, except maybe the vote for upper crust... dont give those crooks your business (and the pizza there is really nothing special any more). From someone that spent over 20 years living in boston eating at regina and santarpios WAY to many times.......Sometimes the regina's in the north end is better, sometimes santarpios is better, both pizzas can be really good, and they are definitely different. If your going to the north end anyhow you should try to hit regina's... but dont bother with their other locations (both pizzerias have been expanding lately). These pizzerias are the pepe's and sallys of Boston and theres an age old debate over which one is better that divides the city. I can see why... they both have good weeks/days and bad ones, and honestly I like them both about the same..... maybe with a slight soft spot for reginas when they really have a good night.
Both pizzerias use the same brand of cheese, they both use high gluten bromated flours (neither one all trumps, which is what most pizzerias use). There is a big difference in the sauce, however. Santarpios uses pastene kitchen ready tomatoes and they pre cook them (blasphemy in the NY pizza world) but its actually really good! The sauce is put on top, and toppings are put on first, so the order for a pepperoni pie goes.... form the skin, pepperoni down first, cheese down next, sauce on next, grated cheese on last. They actually use part skim mozzarella so they can get away with using more cheese before the pie gets too soupy/oily.
Regina's uses whole milk mozzarella (again same brand as santarpios) and a tomato that is custom packed for them by stanislaus thats great, and put in the standard location below the cheese. In their raw state you would prefer the tomatoes at regina for sure.... but sauce on top at santarpios is great if your a "sauce guy" because you taste it more then if its under the cheese. Reginas also has a MAGICAL oil that is used on some of the specialty pizzas pre bake (the polo pesto pizza can be killer at reginas!). You will see bottles of the sauce sitting on the tables for use as a dipping oil, or condiment for the pizzas... its an olive oil, garlic, romano/parm cheese, chilli flake concoction that is highly addictive. They will give you some in to go containers to take home, and I suggest it!
Those are the first two classic pizzerias I would hit for sure.... both slower baked psudo new york style, but with their own twist from each other, and a classic NY slice.
For me Max and Leo's would be a must try as well. They have an earthstone oven thats 100% powered by coal. Its the closest thing to new haven pizza your going to find around here, but they definitely have their own thing going. They bake faster....colser to 4.5-5 minutes, where a new haven pizza usually sits somewhere between 5-10 minutes depending on the time of day (those old coal ovens are tricky). Max and Leo's dont use bromated flour like they would in New Haven, but they do have a fork mixer (nobody in new haven has a mixer like that) which is really the best there is.
Hopefully they are reading this..... Last time I was at max and leo's they were playing with their dough too much to get the edges flat, and the texture suffered a bit. I also had a pie there with some over proofed dough, but when its on its on! Its certainly a monster setup for making a good pie. Sometimes they put on a little less cheese than I would like (and I dont like tons of cheese), but overall it gets my vote for best in boston

Gotta try the coal fired wings at max and leo's too.... they are really good.
Just so you know... all three of these pizzerias use aged not fresh mozzarella. There are some other new places popping up that claim to be doing neapolitan, and I have seen a great review of a neapolitan place called imposto in davis squre by our own john della vecchia, but I have heard some negatives about that place as well...not sure what the deal is on a daily basis.... did he just get lucky? maybe others can chime in. In general, Boston is a bad town for fast baked Neapolitan pizzas, and there are certainly no places putting out the kind of qulaity you would find in the NY area like Keste, Amano, Motorino etc....
Boston is a tiny city, so its really fun to visit. Must stops.....(but omg beware if its really marathon weekend) a walk up newbury street, a walk through the north end, or our Little italy (home of the original pizzeria regina), a view from the top of the prudential center (and or a drink at the top of the hub) a visit to Harvard square, a walk along the esplinade and bike path on the boston side of the charles river. oh god.... there are so many great places!
There are so many great restaurants in the north end, but the only time I have been totally knocked out by Italian food in boston (and I used to eat out a lot!) was at sorellina in the back bay. Its pricey, though. Even with the recent leagalization of food trucks, which has created a mini street food revolution I honestly think boston is still best for fine dining, unfortunately. Its no NYC where you can be blown away by inexpensive food.
I have also been blown away by meals at l'espalier which is crazy expensive, but OMG. Next door to them (they share a kitchen and are under the prudential center) you can get a crave worthy burger and fries at l'espalier without having to spring for the expensive stuff on the menu. Beware though, most of the places I am talking about are ground zero for the marathon!
Away from the marathon area, some other places I have had great meals are The Franklin cafe in the south end (mid priced) Cragie on Main (killer burger here too!) Jojo taipei (very inexpensive and some of the best authentic asian food I have ever had anywhere) Oleana (mid priced) Oh Ya!..very expensive, but insanely creative uber high end sushi.... I could go on and on... let me know what kind of food you like and I can direct you to a place that does a good job with it.
Dont fear staying anyplace thats near a T station (not to be confused with the commuter rail) if you want to get away from the crazy marathon crowd that will be taking over the bulk of the back bay. If you go any other time of the year besides marathon weekend I would suggest staying in Copley Square since its sort of the epicenter of everything, and has lots of hotels in many price ranges. Good luck, and Have fun!!!!