|The title of this article is conjecture based on information revealed in the A Song of Ice and Fire novels or related material and may be subject to change.
The Harpy is the mysterious leader of the Sons of the Harpy. His or her true identity is unknown.
Tyrion and Varys surmise that the Sons of the Harpy must have some central leader and mastermind - given that their escalating attacks culminating in the ambush at the Great Pit must have required a considerable amount of planning and coordination. They can't just be a loose affiliation of local rebel cells.
Vala is later captured, a prostitute that helped the Sons of the Harpy trap and kill Unsullied and Second Sons, and brought before Varys. He gently interrogates and pressures her, asking for information about who the leader of the Sons of the Harpy is. Eventually he gets information out of her using a combination of implied threats, and passage on a ship to Pentos with a large bag of silver (too heavy for one man to carry). Vala, however, did not know the identity of the Harpy leading the rebels in Meereen itself - though she did reveal that they are actually receiving funding from the slave-masters in Yunkai, Astapor, and Volantis.
In the books
In the A Song of Ice and Fire novels, while the Sons of the Harpy didn't directly attack the Great Pit, a running subplot in the fifth novel is that Daenerys and her advisors similarly realize there must be one central mastermind leading the Sons of the Harpy - whom they dub "the Harpy". As of the end of the fifth novel, however, they are no closer to discovering the identity of "the Harpy". This is being introduced now in the TV show - possibly because, in part, prior seasons didn't have as much time to go into more detail about the internal politics of Meereen, as Daenerys tries to determine which of the local rulers is in reality the Harpy.
Major candidates who might be the Harpy in the books were several of the leading families of the Great Masters - particularly the House of Pahl, who lost many sons during her conquest - though Daenerys feared that they are just the most likely suspects.
Another option is that it is one of the local aristocrats who have been the most helpful to Daenerys (worming their way into her confidence just as the Tyrells did to the Lannisters), particularly Hizdahr zo Loraq himself (which is what Barristan suspects), though Hizdahr's death in the TV series at the hands of the Sons of the Harpy would seem to dispel this. Another candidate along these lines is Galazza Galare, the high priestess of the Temple of the Graces in the city who is the greatest voice calling for peace and order under Daenerys's new regime.
Yet another option is that the Harpy might actually be one of the leading freedmen: while this seems counterintuitive at first, the point is raised that some of the freedmen are angry that Daenerys isn't going far enough by completely exterminating all of the Great Masters down to the last child - as seen with Mossador last season, and Daenerys's loss of support among the freedmen when she executed him for murdering a captured Harpy. In this episode itself, Tyrion and Varys see anti-Daenerys graffiti left by the freedmen. After conquering Meereen Daenerys wanted to make peace with the other slave-masters in Yunkai (feeling she was having enough trouble ruling Meereen itself) - re-opening the Great Pit was even a major concession to the Yunkish slave-masters, and she agreed to peace despite having the upper hand for the moment. In several ways, the freedmen angry with Daenerys had more reason to break the peace than the Sons of the Harpy did. Thus it is possible that "the Harpy" is secretly a freedman who is duping the Sons of the Harpy into making counter-productive attacks, trying to provoke Daenerys to kill them all in retaliation.