Looked at your file.....

Image 1) in this image, we can see extra edge. Just as a rule of thumb, you probably don't need these and if you can get rid of them you should. I saw several places in your stcuture where these appeared. They mess with the normals sometimes, make file sizes larger than what they should be if you have enough of them, and can cause a number of small problems in the future if you decide to tweak your model somehow.

Image 2 and 3) After selecting and deleting the edge, there are leftover vertices where the top and bottom of the edge existed. You can view them by displaying them. (right-click and hold over your model and select vertices) You should select these and delete them after you delete edges to ensure future problems will not pop up.

Image 4) As you can see, there are three little square-like dots. Since you're new at Maya, I don't know if you realize this or not, but these are faces. (right-click, select faces from menu) There should only be one of these present. You probably accidentaly made two more when you extruded of something, but didn't pull the face out when you did. Not sure really.

Overall, you should always try to keep your models clean by deleting these extra things.

Now to solve the boolean problem.....

The easiest way for me to do this was to delete some faces from your Main Structure. I deleted all the faces where the wall was. This created two holes in your model that needed to be filled. You can automatically fill these holes on this particular model press choosing EditPolygons>Fill Hole under the Modeling Menu.

Now we basically have an open end of your house. To fill this in, we create another cube, scale it so it looks like your wall, then position it in it's proper place. We can now boolean properly and your window will be created.

Image 5 shows that there are three objects - your main structure, the single wall (the cube we created and scaled to look like your wall), and the Window Boolean which is the object you will use to boolean the window out.