Maybe I'm jaded through such places as Pepe's and Grimaldi's but I found Santarpio's, while very good, to be a definite step below.
First, their cheese is not fresh like Grimaldi's. It's standard cheese that you'd find in any pizza store around the country.
The sauce tastes like a sweet tomato sauce that you'd put on spaghetti. A pizza sauce should have a slightly tangy sense to it.
The crust was a bit thick for my tastes, and the cornmeal, or whatever was sprinkled accross the bottom didn't add much to taste and adding an annoying texture to each bite. Also, the crust was not cooked enough, with the bottom looking very white, not charred at all.
Best pizza in Boston is definetly Galleria Umberto. In fact, that is one of my favorite pizza stores anywhere, and the countermen are really nice.