What's a Windows key?
My Ctrls and Alts are single-key sized and tucked together next to the spacebar. I don't know if it's better, it's just what I'm used to.
For Ctrl, it seems sometimes I use my thumb, sometimes my pinky, sometimes my ring finger. Probably depends on the key combination. Left-Alt seems to be just the thumb, but Right-Alt is either thumb or ring finger. Always opposite hand, though; I gave up the same-hand habit when I gave up the WordStar-compatible editor commands. I've gotten so soft in my old age.
On a more standard-layout board I stick to pinky fingers for Ctrl and thumbs for Alt, but I spend as little time as possible on one.