A couple of tips that seem to work well:
(1) to kill the internal reflections off the window, use an adjustable polarization filter over the lens. This however, sometimes has the undesired effect of generating polarization “rainbows” if there are scratches in the plexiglas (other times, the rainbow effect actually enhances the picture, but I suspect that in the type of document photos you’re making, it may be a problem).
(2) Make your photo pass away from the sun, so the light comes from behind the plane / photographer.
(3) make your pass course far enough to the left of the ground object so the pax/photographer, sitting in the front seat can see it through the windshield and continue to see it out the door window as you get closer (lets him/her get it framed up well). As you make your closest approach, roll right and add in left rudder to keep the plane tracking straight but right wing low so the photographer has a clear shot (no wing in the view, small angle between the lens and the window as the photo is taken.) Remember, this is a cross-control situation, so be careful, keep the speed up and watch your attitude! Alternatively, make a moderately steep turn 360 to the right with the ground object as your turning fix, and have the photographer make the shot as the light comes from the correct direction.
(4) If you’re making “horizon” photos (low altitude with the object apparently high in the window), make sure the light is coming from the pilot’s side…
This may all seem elementary, but it took me a while to get even these things right! [:)]