What is the difference between my seat is by the window. and my seat is near the window. ?Feel free to just provide example sentences.

My seat is by the window - there is not another seat between mine and the window. My seat is the closest.
My seat is near the window - Your seat is close to the window, but there is at least one seat between you and the window. If there is a window seat, a middle seat an aisle seat, all three of them are near the window (all three people seated there can reach out and touch the window), but only one seat is by the window.
The difference is that a seat by the window has nothing between it and the window. A seat near the window can have things between it and the window, but is still close to the window.
It doesn't matter if the space is large or small. There will be some seats that are by the window and some seats that are near the window, but not by it. Of course, there can be seats in the middle of a room that are neither near nor by a window.