First off, the obvious: The Harpy in its mythological connotation is female. The (male) Meereenese nobles who are waging guerilla war against Her Radiance are referred to as Sons of the Harpy. If there really is a "head" figure in this guerilla war and they're not just a bunch of independent sleeper cells, it makes sense that the Harpy in question would be a woman. But it never occurs to Dany, herself a woman allegedly ruling a city, and her advisers that this is a possibility.
Dany's advisers are convinced that Hizdahr (who I think is a slug but ultimately just a pawn) is the Harpy, because "he" can get the violence to stop when Dany agrees to marry him. But who suggested to Dany that she should marry Hizdahr? The Green Grace.
Dany starts getting paranoid about the prophecy, thinking, for instance, that Reznak is probably the "perfumed seneschal." Yet she lets the Green Grace have access to her with pretty much no hesitancy or suspicion or wariness whatsoever. Even though she's a Ghiscari high priestess with significant cultural and familial ties to the city — she seems to defend the rise of the slave culture, saying that the area had no other economic prospects; she tells Dany to her face that she's seen as an invading murderer; she's intimately aware of each noble house and the differences between them. By giving Dany "helpful advice," she also has access to most of Dany's plans and strategy, and as such would know the easiest way to exploit any weaknesses. Dany tells her exactly who's moved against her and how (i.e. Qartheen ships doing a blockade). The Green Grace knows when freedmen have been killed, "or so she's been told." She also knows that Dany would never kill the child hostages — namely that she and her agents can wreak havoc without worrying about losing anything.
She also moves pretty seamlessly between the nobility and Dany's court — it seems to me that if she were actually helping Dany, she herself would be a target and treated like a collaborator. But she isn't. Why? Because she's not actually helping Dany.
Finally — this isn't exactly evidence, just a bit of irony — it'd be hilarious if the people that Dany's really suspicious of were actually loyal to her while the woman she thinks of as a close confidante is actually the one working to destroy her. Oops?
Edited by Apple Martini, 19 December 2011 - 01:46 PM.