There was Foxy Brown. She's the closest IMO. I'm not counting the first two albums as some of the material was penned by Jay, but Broken Silence is about the closest that Fox got to being the female Jay without him penning her rhymes.
I don't count Lauryn Hill because her subject matter and content is more along the lines of Talib, Mos Def, and Native Tongues than it is Jay. Her flow is also more spoken word. Foxy explored some of the same subjects as Jay and had more of his flow and swag.