Before the drug war the metro area of Toluca was by far the most violent city in Mexico for females and not Ciudad Juarez as commonly believed, in fact, when cities are ranked by their age-adjusted homicide rates from 1990 to 2006 (right before the drug war started) Juárez was not much more violent than Mexico City (Valle de México in the chart).
To construct the list I used the metropolitan areas as definied by the INEGI
plus a made up metro area of the municipalities of Culiacán and Navolato, I also included municipalities like Durango which are not part of a metro area but have a population of more than 400,000.
Since violence in Mexico was declining before the drug war
it is also worthwhile to take a look at the yearly rates:
Notice how if we look at the drug war years Toluca actually had a lower female homicide rate than Monterrey in 2010, which used to be the safest metro area in Mexico.