No, you can't say that. If you mean 'through the window' you have to say 'through the window'. If you say you can see something 'in' the window it means you can see the reflection of something: 'It was dark outside so he could see the reflection of his face in the window.'

It's OK. I was trying to think what I would say spontaneously. Perhaps I would say sometimes "I can see the moon in the window." If I could only see the moon through the window while very close to the window, I would say : "I can see the moon from the window". For some reason, it feels more natural to say "I can see" rather than "I see". You might say "I see" in response to the question : "What do you see when you look out of your window?"