Have you read the Scholomance series by Naomi Novik? It's very good.
The main character is definitely an antihero, though I don't think she does anything particularly amoral. (She's actually one of the most idealistic characters in the series, but has the cards very much stacked against her.)
She's also very capable (might verge on Mary Sue territory for some, but I like competent characters) not particularly charming, has a dark sense of humour that I find very funny, and - oh, I'll admit it. I have a crush on her. There, it's out