The Expanse series has Naomi Nagata, Avasarala, Bobbie Draper, and Drummer (among others)
The Revelation Space trilogy by Alastair Reynolds has the badass Ilia Volyova (cyborg space pirate; it makes sense in context lol) as a main character (not primary protagonist though) in the first two books and Ana Khouri (ex-military/assassin) is the primary protagonist in the second two (and major character in the first).
Some of Reynolds's other works also have strong female protagonists as well (e.g. Pushing Ice and the whole Revenger series). House of Suns is one of my favorites, and there are two protagonists, male and female, and have equal spotlight throughout.
Both of those are hard sci-fi, so hopefully that's your jam.
Try out the Wayfarer's series! Becky Chambers is amazing. Her books are wholesome and character focused, and give you a great feel of what it would be like living in that setting.
I also really like Brandon Sanderson's Cytoverse. It's a fantastic adventure that will keep surpsing you, but it is YA, so be ready for a little silliness.
Shatter Me by Tahereh Mafi (Young adult dystopian scifi)
Across the Universe by Beth Revis (Young adult)
Bird Box by Josh Malerman (apocalyptic thriller)
Mistborn by Brandon Sanderson (fantasy, not scifi, but I'm digging up stuff from when I used to read more prolifically)
Revelation Space series by Alastair Reynolds. I read this so long ago, and I feel like their were some great female characters, but I can't remember if any were the protagonist. Each novel shifts around.
Xenobiologist Kira Navárez in To Sleep In A Sea Of Stars might not win feminist awards, but I really liked her, the world building and the story. IIRC, it was relatively clean of overly sexist BS.
Echoing what others have already said here: The Expanse. The depth and quality of pretty much all the main characters is great. And there are several fantastic female characters who are strong, smart, and wonderfully written.
The Steerswoman series by Rosemary Kirstein, and the Merchant Princes series by Charles Stross—both series that may not seem like sci-fi at first, but become increasingly so as they progress.
I see lots of good picks here, a few of my favourites books mentioned... I love The Expanse in particular, but "Pushing Ice" by Alastair Reynolds had a better focus on complex female characters.
Well my first recommendation was going to be Ancillary Justice, but there’s also Artemis by Andy Weir! It’s been a minute since I’ve read it but I don’t immediately recall it snacking of a “men writing women” feel.
Edit: Not super SciFi, but like steampunk fantasy maybe… Another option might be Mistborn by Brandon Sanderson.
Second Edit: Whatever you do DONT read Hyperion. Oof that one was one of the most ridiculous examples of “men writing women” I have read, although he notably grew as the series progressed.
The Iron Widow by Xiran Jay Zhao.
Think Neon Genesis Evangelion X Female Rage X Chinese History. It's by no means a perfect book, but it's entertaining, the premise is very interesting and the character work is quite good!
Chinese "history" in this case being pretty questionable, but Wu Zetian is always going to be a natural target of more or less accurate revisionism, and if there's one thing we know about her for sure it's that she was already the target of patriarchal revisioning.
Look, at this point I'm basically just "That guy who recommends the Luna books", but this is yet another situation where they really are the right answer. Luna: New Moon is your starting point. The series is absolutely bursting at the seams with diverse and interesting female and non-binary characters. It also features some wonderfully atypical male characters who really play around with our understanding of what it means to perform masculinity. I am obsessed with Lucas Corta, iron fisted patriarch whose one weakness is for the beautiful young man who plays bossa nova for him, and I'm equally obsessed with his son Lucasino, the rich kid playboy who has fucked his way through his entire friendship circle, and loves makeup, androgynous clothes and baking.
Anyway, Luna: New Moon by Ian MacDonald. Give it a look.
Definitely worth it to keep reading. He's finished the series now, and the payoff is solid (personally I felt he could have gone for another book, but I really like the ending he chose).
I liked the Academy/Priscilla Hutchins series by Jack McDevitt. Character drama isn't necessarily a big part of it, partly because most people act like real humans (for sci-fi) and it's more about the space exploration angle and, on the series level, about how that changes over time.
Damn, took mine. Although thanks for saving me a google, since I have a terrible memory. Not a female, but very similar stories are his Alex Benedict series.
I had so much fun reading The Adventures of Amina al-Sirafi by Shannon Chakraborty. It is squarely in the fantasy genre. Not SciFi like you're asking for. But I can't recommend it enough.
Amina is a very rare character: she is simultaneously an older woman, a single mom, a pirate, a lover, and a legendary hero. Chakraborty does an admirable job of balancing all these different aspects of her main character's personality. The story is bombastic and fun, the supporting characters are charming, the setting is historical and fantastic all at once. This book is incredible, I could not put it down.
I have heard good things about the audio book. I read it in text form though, so I can't confirm that myself.