I've had people make snarky comments at bars and breweries and I'll usually reply back with a comment of my own, something along the lines of "is there a problem?" Not in an aggressive tone, but in a serious one. I am not a confrontational person in any regard, but given it's a sensitive topic I do take a bit of offense. Plus, it's a personal thing - weird to comment on.
Obviously in the workplace you want to avoid escalating things. I agree with what others have said about mentioning that there's a men's restroom for use as well. I'm not one to tattle either, but if this persists, maybe think of speaking to HR.