Carolyn Seymour is a perfect choice -- she was a badass Romulan commander, why not a Federation one? (Sam Jackson can do anything he wants, but somehow I feel like I'd be waiting to hear a Starfleet Captain use the word "motherfucker."
TSC, that's a really strong list of female candidates. Cate Blanchett, Lena Headey, Charlize Theron, Gillian Anderson are all definitely certified with the necessary charisma and energy. Linda Hamilton and Sigourney Weaver too, although I admit I have trouble separating them from their pre-existing action-icon roles. (I have the same deal with Amanda Tapping, who built a great scientist character on the original Stargate but who I came to identify so much with that role that buying her as a commander got harder. Probably totally unfair, but it's there.)
A couple of the others I haven't actually seen in action (Anna Gunn, Reiko Aylesworth). I also have a feeling Jessica Chastain should maybe be on a list somewheres? But that's mostly on the strength of her look and her rep from Zero Dark Thirty, which I haven't actually seen. There's a couple others like that -- Annie Ilonzeh is another one who just looks
right but I don't actually know anything about.