Strangely enough I'm a private pilot and also a part-time professional photographer. Thought I'd give my two cents...
Lens selection I use a 70-200mm IS 2.8 L and sometimes switch to my 17-55 2.8 for the "experience" photos. I would like to say IS is a must, but I squeaked out some good photos with my kit lens before I built up my lens collection. The plane will be flying slow, so the engine will be at low RPM, and therefor you will have more vibration than normal flight. Still, I find the best photos are taken around 80 knots (slow). You can get sharp images at 1/500 and slower without problems.
Filter/Window As others have mentioned, a polarized filter is plus. The reason that you may have better color shooting through the windows is because there is usually a UV or polarized coating on the windows. This is why the FAA frowns upon pilots wearing polarized sunglasses (looking through two polarized surfaces doesn't go well). Unfortunately, you have to choose between window open with a filter, or window closed with no filter or just a UV filter. The best results will be with window open. Worst case scenario (through window) make up a shroud that you can position around your lens to eliminate any reflections on the glass. Some gaffers tape and cardboard can look pretty professional, just ask some of the DIY studio photographers ;) Also, only use the side window unless your goal is to get the dash in the picture. It's unsafe to compose an image out of the front and at the shutter speed needed to avoid the prop, you won't have a good image.
Image stabilization Make sure to leave all IS on. If you have a lens that allows strafing IS, don't use that mode. Remember, the IS senses movement of the lens. It's technically staying still in the aircraft during unaccelerated flight.
Aircraft position Most of my photography is around 2000ft AGL (above ground) or below. When working with structures, remember your elementary 3D art classes. Shadows don't come straight at you, they generally fall back and off to the side. You need them for depth, so don't shoot at noon or directly between the sun and your subject (noon rule goes away the further you are from the equator).
Plane selection (I don't bother to try helicopters because I'm not licensed to fly those) While I shoot with a C172 or C152, try to find a C177 or another high-wing plane w/o struts and retractable gear. If you aren't doing the flying, your pilot will greatly appreciate not having to do your composition for you (which would happen if you have struts). Plus you will have more "time on target" as we call it in the military.
Weather. Regardless of everything else, you need good weather. If your subject is on the ground, you'll waste money if the skies are more than 50% clouds (waiting for the lighting to move. If your subject is the experience (aircraft in the picture or lots of sky), you will want around 25-50% clouds. Zero clouds with sky in your picture rarely looks good. While on the ground it looks nice, in the air you are looking through a lot more "sky" when viewing horizontally and the color isn't the same as on the ground. Meteorology demonstrates that vertical cloud development is mid-late afternoon, so plan accordingly. "Poofy" clouds look amazing from an aerial perspective.
Time of day Golden hour doesn't apply in aerial photography. If you are on the ground, you get nice soft lighting and soft shadows, but from the air you are trying to demonstrate depth, in which case those shadows are your friend. It's a lot more about aircraft position rather than golden hour for lighting. Your canvas is much larger than a person and your perspective is unique only to this type of photography. Tip: if you want some clouds in your shot without the sharp shadows on the ground, ask your pilot to look out for weather with visibility around 10 miles. This means that the weather is giving you an artificial diffuser :) Rarely you can also shoot good shots with a very thin overcast.