Wow, good on you for bringing up The Boss from MGS3. It's one of those characters you tend to forget about, probably because of just having a single outing in a game and because of the MGS-series not exactly being known for powerful female characters!
As for me, there are so many that have already been brought up in this thread. I love Hawkeye from Full Metal Alchemist. Mikasa and Annie from Attack on Titan. Furiosa, Buffy, Liv from iZombie, several from GoT.
But my number one favourite and probably my first crush since I was a kid:
She's cool, powerful, calculating and hidden inside a metal encased suit. But she's still able to show compassion and evoke emotions from just a glance and her actions.
This comes especially from her outings in Zero Mission, Fusion and the Prime-series. Man, I was head over heels ever for Samus ever since the first Metroid game on the NES even though I didn't realize she was a woman til that end scene...
Don't even talk to me about (the story and portrayal of Samus) in Other M though. We will not have a good time...