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.