Judit Polgár is the one I believe. Just checked by cross-referencing http://ratings.fide.com/top.phtml and http://ratings.fide.com/top.phtml?list=women. Could well change in the coming decades, but competition is currently mostly separated into men's and women's divisions, like other sports (most top women compete for the Women's Chess Championship, though Polgár is a notable exception in never having entered that tournament).

edit: Was curious to look a bit more, and it seems like the reason is that there are currently very few active women in competitive chess to begin with (i.e. it's not that there are many outside the top 100 either). For example, there are 1574 Americans on the FIDE active player list, of any ranking (all the way down to rankings in the 1300s), and of those, 1491 are men and 83 are women.