there is nothing in boston anything like patsy's. My suggestion to you is to take Boston pizza for what its worth as its own thing. Here are my rec's
Posto.... The only pizzeria here using a wild yeast starter. They have a high temp oven and their pizza times in at right around 3 minutes just like Patsy's (3-4 min). Their lean is more toward neapolitan, but its the closest we have to a patsys type of pizza. I have heard it has been getting better and better since it opened. Its in davis square, which is a fun area.
Picco..... A decent attempt at artisan pizza, so really great toppings but normal 550ish oven temps. Home made ice cream too.
Pizzeria Regina north end location. I like this pizza better than santarpios, which can be too chewy for me at times. These two pizzerias are always in a battle for "best of boston" and have both been around forever. Regina still has the original 80 year old oven, which is pretty cool. They both are normal temp (550 degree) pizza. Pizzeria Regina is in a must see area of boston, our "little italy".
Not to knock marc's suggestion, but tripoli while having a REALLY sweet sauce, isn't much better or different than the pizza at my high school cafeteria. If I was going to drive for pizza it would be to "brick" in new bedford, which in my opinion is the best pizza in Mass/RI/NH
Nothing else comes to mind that stands out above the rest.