Two of my best friends are pilots for American and I can echo that the "least" bumpy area on a plane is over the wing or the middle of the aircraft. Turbulence, especially clear air turbulence, isn't really a problem that's going to make you crash unless the pilot is an idiot and flies directly into a thunderhead.
My first cousin is also a maintenance supervisor for Delta and laughs about the allegations of the "air quality" on planes. Most of the air is pulled in from outside and that, and the recirculated air and oxygen, is heavily filtered. There is no control over having "Typhoid Mary" or "Swine Flu Flo" sitting next to you but the air isn't the problem. They do not sanitize the tray tables, buttons or other things on the plane. I use a Lysol Wipe to wipe down the tray table.