I had to pluck the remaining glass [...] the window frame.
What's the correct choice and why?
"From" is the only correct choice from the three you offered, but you could also use "out of" (note, one "f").
I don't think there's any rigorous reason why; it's just the way native speakers would say it. That said, the glass in a window does sit inside the frame, so removing it necessarily involves taking it from inside to outside, or out of the inside to the outside.
P.S. I wouldn't typically use "pluck" in this situation (I'm assuming it's a broken window, where most of the glass has gone, and you're left dealing with the pieces still stuck in the frame). "Pick" might be better, or just "remove".