I think the key is for all store owners to create a welcoming environment for all people. Not just women. The tone of a business is set by the owners and the employees. If for no other reason than it's good business sense. This past June I was in NYC for several days. I did drop by some comic shops while I was there. I had great experiences in some like the Midtown shop on 40th, JHU, Forbidden Planet and Toy Tokyo.
For example, the back issues I was interested in were't located in the Midtown on 40th and I was leaving the next day. The employee showed me their ad in one of the new books and had me write down their online coupon code and I went back to my hotel and placed the order.
On the flip side the attitude that I received at Carmine St. and St. Mark's was ridiculous. I guess I didn't look cool enough to belong. In Saint Mark's I asked about a particular title, and the guy told me that "If you don't see it, we don't f'n have it" Seriously? Perhaps it was just a bad day at both shops.
My local shop has one very negative review on Yelp from a woman detailing her several negative interactions with the staff. Not sexist or harassing comments, but what she feels is subpar service because she's a woman. I find this baffling because I have never seen any of the staff treat women as she describes.