訳:I see you through the window.
No, that sounds like the person is above the window. The best and most common way to express the meaning is "through the window".
"I see you on the other side of the window" has a similar meaning, but I don't know if it's a good translation of this sentence.
Thank you No-one. The Japanese sentence 「私はその窓越しにあなたを見ます。」means just you writes. 「私はその窓越しにあなたを見ます。」=the person is above the window. and you see him/her.