Their is no strong mafia presence in Baltimore at the moment, though I have heard the Gambino's had a faction there for some time. As the years have gone by, the Mafia's interest in expanding to smaller city's seems to have waned, so don't expect a mafia presence in Baltimore anytime soon. From what I can tell any notion that Greeks run Baltimore can be squarely put on David Simon's shoulders.
The real and somewhat anti-climactic truth is that their is no over-arching organized crime group that "runs" Baltimore. The largest crime groups in Baltimore are street and prison gangs. The Black Guerrilla Family is probably the most powerful of local groups due to their size and tendency to use violence. They are also the most organized of the Baltimore street gangs thus allowing them to make money hand over foot in the drug game. That being said, the life expectancy of a BGF member is getting lower every day as more and more of the city's violence involves BGF members.
Besides the BGF, other large gangs are the Bloods, though they are extremely unorganized, with interfighting very common, the Crips, who have are in a similar situation as the Bloods but are a much smaller presence, and the Caucasian prison turned street gang Dead Man Inc. aka DMI. The DMI were created fairly recently and have grown exponentially in the last few years. DMI are concentrated mostly in South Baltimore, in the Curtis Bay area, where Caucasian populations are larger.
Overall Baltimore is a city full of independent groups, which is a major reason for the explosion of violence, with no order it's a free for all. Gangs stick to the drug and weapons trade, as well as other blue collar crimes (robbery, car theft etc.) White collar crimes are run by individuals or small groups, for example their is no large scale group running illegal gambling machines, instead small business owners, usually Asian or Indian ones, run their own gambling machines in a small number of businesses.
Other organized crime groups, such as Hispanic gangs like the MS-13 and Latin Kings operate mainly in neighboring counties, while Biker groups such as the Hells Angels, Pagans, Warlocks, Outlaws, and Iron Horsemen MC's tend to mostly operate in neighboring counties as well, especially on the coast. Neither groups have a very prominent presence in the City.
I'm sorry to have given such a long-winded post, but I've seen this question posed several times before and I hope this could put to rest some people's curiosities.
Source - I'm a Baltimore crime reporter.
