Easy! As a pilot, I can tell you the best seats. The two up front!
But I digress. Unless you are just looking at documenting your trip, on commercial airliners, there aren't too many spots for you to take photos with much "wow" factor. A couple factors contribute. First, in order to decrease stress on the airframe from compress/decompress cycles, the windows on airliners are designed more like ship portholes making your field of view extremely limited. Second, this makes most compositions pretty boring as we've all seen them before.
For normal documentation shots, I would try to find a seat that doesn't sit over the top of a wing or beside an engine (fuselage mounted). Otherwise, they are pretty much all the same.
If you want some aerial shots with more wow, I would recommend going to the local airport and renting a plane and pilot. A small aircraft offers wonderful compositional opportunities. It has much larger windows (some don't have any or can be removed) with a much larger field of view, flies at a lower altitude, and cruises slower so you can have more time to get your shots.
Hope that helps!