We do use "at the window" occasionally, but only in one quite specific situation that I can think of, which is a person (perhaps also an animal) standing at the window (looking out, or looking in). Maybe also a moving object like a car which stops at the window.
Thinking about it, in both cases the correct synonym is actually "by the window", not in it. On balance I think that "at the window" is an incorrect translation of the Hungarian.
I've never heard of “in the window" in this context. I would say "on the window".
"On the window"would mean literally on top of it - sitting on the frame, or if the window was horizontal for some reason, lying on the glass. It is perfectly correct gramatically but only used in very specific situations, and I'd imagine it would require a Hungarian postposition or suffix to indicate the specific position.
If you're trying to say that the apples are visible just behind/in front of the window, as in a shop display, then "In the window" is definitely the correct term in English.