If your interested in trying my pizza I have a restaurant very close to Fenway park and another right by Harvard Square, two of the areas you mentioned visiting. They are called Stoked Wood fired Pizza and Stoked Pizza. Definitely shoot me a heads up via PM ahead of time if you end up doing that.
My favorite restaurant right now is probably Oleana. It always totally knocks it out of the park. Its not a vegetarian restaurant or anything, but I never knew vegetables could be that good. Its worth the drive even if its out of your way a bit.
https://www.oleanarestaurant.com When im in Salem I usually hit Turners Seafood.
https://www.turners-seafood.com. Its also pretty hard not to bump into a Legal Seafoods when your in town with all their locations, but dont let that scare you. I have never had a bad meal there either.
For pizza, Pizzeria Regina in the north end has never let me down, and I think you will be in that area. Its sort of a cross between NY slice style pizza and classic sit down coal fired NY pizza (but its not a coal oven). I used to really like Santarpios, but I have had quite a few bad pies there over the years so I havent been there in a while. I really like Area Four and Picco. I havent been, but I have heard great things about locale (also north end) and brewers fork (very close to north end). For Neapolitan, my favorites are Rossopomodoro (located in Eataly), Posto, and Ciao pizza and pasta (right by the airport).
Rinos place (with the ddd link) is for sure really great. If its hard to get in or out of your way there are also a lot of spots in the north end that I think are right at that same quality with similar menus.
I think you will really enjoy your visit.