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.