Foodwise, Baltimore is most known for its crabs, crabcakes and, to a lesser extent, pit beef. Being from Maryland and having lived in Baltimore City for the past two years, I can tell you that there is very little in the way of good pizza.
My first choice for pizza is to make it at home using the tips, recipes and techniques listed on this website. My first choice for pizzerias is a place in Mount Vernon (a neighborhood north of downtown) called Iggie's Pizza. They make a Neapolitan-style pizza that is ok. It's kind of expensive for about an 8-10 inch pie, but it's probably the best option in town. They have pretty good combinations of toppings and the crust is ok (a little flat and lacking any real char considering it's baked in a wood-fired oven). I like the place, though, b/c it is BYOB and has a really cool, laid back atmosphere.
Two other places in the city that are worth mentioning are Joe Squared and Zella's. Joe Squared is in teh Station North neighborhood. The pizza there is ok. The toppings are good and the pizzas are baked in MD's only coal fired oven, but these pizzas are not nearly as good as those baked in NYC coal fired ovens. Nonetheless, the pizza is pretty good and, like Iggie's the atmosphere is great (they have live music most nights). I haven't been to Zella's, but I've heard that it's pretty good.
Outside of the city, there is a place called Pizza (not Papa) Johns, which is in Essex. I haven't been there either, but it is supposed to be pretty good.
Other than the above, there is not a lot of good pizza in Baltimore. That is one of the reasons why I have started to make my own. Let me know if you have any questions.