As a huge fan of contemporary progressive jazz, there are no problems finding plenty of women instrumentalists, with major chops, in various subgenres of jazz.
Here are a few off the top of my heard.
Mary Halvoerson - avant-garde guitarist. Very prolific, plays with various ensembles.
Ingrid Laubrock - great sax player, quite creative.
Tomeka Reid - virtuosic cellist. Very creative.
Janel Leppin - another great cellist. Inhabits what is often referred to as "chamber-jazz" with her group, Ensemble Volcanic Ash.
Muriel Grossmann - Austrian sax player. Best classified as "spiritual jazz". Hints of Alice Coltrane.
Hiromi - fusion keyboardist, with terrifying chops.
Mohini Dey - fusion bassist. Literally one of the best bassists on the planet. There are videos of her at the age of 11 performing with her father, and she embarrassed most electric bass players then.