Agnes Varda had most votes in the poll of top 5 films by women conducted by Senses of Cinema (excellent online magazine). Unfortunately it does seem the case that few- if any- female directors have to their credit more than a couple of films generally deemed great.
Perhaps if a poll were to be made of favourite films of international female critics, more women would come to the fore.
The extraordinary, precocious Samira Makhmalbaf seems best placed to build a huge reputation. Iran has had a high percentage of top females; also her aunt/step-mother Marziyeh Meshkini, the poet Forough Farrokzhad, and Rakhshan Bani-Etemad. Perhaps India's Mira Nair (Monsoon Wedding) can continue to develop.
I especially like:
Madchen in Uniform (Sagan), The Ascent (Shepitko), The Silences of the Palace (Tlatli).
The Bulgarian film The Attached Balloon, directed by Binka Zheliazkova, is- in my imagination- the most fascinating and wonderful film ever made, (after Sansho the Bailiff, of course).