Far too often in comic books, a super heroine only becomes empowered after being raped or assaulted, and wanting to become stronger to never let that happen again. I think future female superheroes will have to have origin stories NOT involving a man ruining their life. Something like a freak accident giving them powers, naturally superhuman abilities (maybe they're an alien? Or part of a mythical race), and the simple desire to be stonger or make a difference in people's lives.

Also, female superheroes seem to have a knack for getting captured, despite, you know ... being superheroes. I'm not saying a character should have no vulnerabilities, but I think that there should be challanges that need to be overcome rather than putting her in a position where she's helpless.

And for general character-making, I think it's important to make the character a feminist without using the word "feminist." You don't want to sound preachy or turn off less enlightened readers, so it's better to just make a compelling character who's intelligent and strong, and let your lack of traditional gender stereotypes speak for itself.

You could work in other themes you believe in to make the story richer. Pro-animal rights? Maybe your heroine is an activist, and your comic chronicals both her work and her struggles to make her family understand why it's important.
Also, you could work in characters of different religions, ethnicities and genders who don't just become the token (insert group). Comic book characters do tend to be a sea of pretty white people. I think breaking that norm and having a diverse cast will make readers appreciate your work for portraying a world that's closer to our own.

Best of luck in your work!

Hmmm... I suspect the TV Tropes Wiki will have something appropriate to say.

Ah, yes...

http://tvtropes.org/pmwiki/pmwiki.php/Main/MagicalGirlLyricalNanoha

Not exactly a comic book, but the heroines in Hayao Miyazaki's films always inspire me... but they are not without their problems (a bit too self-sacrificial...). To me, a feminist heroine has to go beyond the 'oh wow she can kill people' idea (I'm not fond of feminism being about women taking up the most destructive of traditionally 'male' characteristics, I think we have to get away from that violence = strength mentality in general rather than just expanding it to women) and be somehow non-violent as well as super-hardcore. I think the character of Nausicaa from 'Nausicaa of the Valley of the Wind' does that well, but I do get annoyed at her sweetness.

In terms of physical appearance, I think her biceps and quads should be bigger than her chest (assuming your are creating an action book, not a drama.) Her clothing should be what an actual PERSON would want to wear whilst kicking ass: loose t-shirt, pants/shorts you can actually move in, boots with NO HIGH HEEL. Close-up images should emphasize the muscles in her back or the tendons in her hands, rather than a pre-pubescent stomach or startled eyes. It would be great to use actual female athletes for inspiration: runners, skiers, martial artists. Any athletic sport that emphasizes performance over appearance. (So NOT ice skating, gymnastics or cheer leading. Those women are incredible athletes too, unfortunately, their body shapes play too big a part in how they are competitively rated.) What does a female athlete look like when all she cares about is how fast she can run, how hard she can hit, how fast can she turn?

I realize focusing my commentary on her appearance is a bit shallow, as it continues to emphasize appearance over character. However, I only have a passing familiarity with comic books and not too much to offer re: plot and character development. I really love all of the posts above, especially Ren's point about omitting the word feminist. It's better to lead by example than lecture. It would be cool if she were a conflicted character (Batman, Wolverine) rather than a straight forward do-gooder (Superman.) I think the quest to practice feminism frequently eliminates the easy solution to problems. It would be great to see a female character that struggled with moral questions, and not in a "gee, how do I have a career AND a family" sort of way.

Best of luck!

I'm also an aspiring graphic novelist! Yay!
Just make her human (a female protragonist). Nothing more, nothing less. Males don't seem to be concerned with what kind of "message" they send; they just make interesting, human characters that also happen to be superheroes (or not, if you read non-superhero graphic novels).
As for appearances, most men and women in comic books are idealized, and I actually have little problem with the bodies themselves. I just have a problem with the way the women are positioned with those bodies. Vamping, dressed skimpily, posing for the male gaze...it's not necessarily that she has a D cup, it's that she's pouting sexily at the "camera" whilst showing off her massive cleavage.
That being said, my female characters are not super-hot idealized amazons with wasp-waists. They're just people. Some are pretty, some aren't, some are different.
My recommendation: Castle Waiting by Linda Medley. The only downside is she never finished it. :( But it is an excellent, very feminist work.

Humility, Humor, Humanity. No apologizing for failure or success. No Mary-Sues. (Perfect, desired by everyone.) The fact that she's a woman is incidental to her awesomeness, not an essential part of it. Her personality and identity is more important than her gender.

As far as bodies go, breast size appropriate to rest of build (as in if she's curvy everywhere, she's curvy everywhere. Or if she's petite, she's the expected petite.)

Basically, what women turn your head when you pass them on the street? Is it always women in less clothes or was there someone who walked with so much authority that you took notice anyway? That's what I'd focus on, rather than physique.

First of all, from a storytelling viewpoint, I want to echo pretty much everything Ren said, especially the last point about the surrounding characters. Every hero(even a loner like Batman) is surrounded by a collection of supporting characters in the form of sidekicks, partners, villains, "civilian" friends, pets, etc. The composition and behavior of this group's members offer you as an author all sorts of opportunities to explore different progressive values. Who are the most math/science literate people in the group? The best at combat? (And why are they the best - superior strength, reflexes, intelligence?) Who are the most compassionate? Who practice what faiths? Who come from what socioeconomic backgrounds, and to what effect?

Particularly valuable for study here (though not exactly superheroes) is the ensemble for "Firefly". (Standard caveats about the imperfection of this apply: the captain is still a straight white male, pretty much everyone is stereotypically "beautiful", generally patriarchal social structure, heavily white cast, etc.) Here we have a group of characters, each of whom has an interesting combination of strengths and weaknesses. My favorite example here is Kaylee, the ship's mechanic. She's small and petite (though the character was initially meant to be quite curvy, the actor they cast is naturally very petite, so even though she gained weight for the part, she's still pretty small), with a love of all things cute, and provides a lot of the positive emotional energy for the group. She's not into combat (clearly uncomfortable perpetrating violence against others), which can be a liability in a violent society, but she's generally acknowledged as one of the best mechanics in the 'Verse. Also, while she could have quickly become the innocent-cute one (with mechanical skills), she's also got a very down-to-earth (or whatever planet is nearest) sensibility - she cusses, drinks, and has no real hang-ups about sex.

Which is a rather long way of saying, for maximum impact, make sure that supporting characters are well-designed and complex. Not only does this make them more interesting in their own right, it creates new dynamics for your hero during their interactions with the rest of the ensemble.

As for physical presentation, I'm a strong supporter of the trenchcoat (or other long coat or cloak) left unbuttoned and loose - it allows you to give some dramatic flair to your character's movements without needing to emphasize their figure much. They're also pretty cool-looking and relatively adaptable to time and place. Also, pockets.

When out of such a coat, Jrant's advice is excellent, especially if this is a powerless hero. If she is rocking some powers, the nature of those powers may decrease the need for as specialized a physical build, giving you greater latitude in choices. (Powers being another area to mull over, of course. I'm a fan of non-mind-control augmented mental abilities - better recall, faster thinking, better ability to identify and analyze small details, etc. This allows for more interesting combat, when combat occurs, and encourages you as an author to develop plots that do not rely primarily on brute force contests, which are overdone as is.)

This has become much longer than I set out for it to be, so I'm going to wrap up. Needless to say, you've raised a really exciting topic here!