Who has final authority over Air Force One? U.S. FAA FAR 91.3 ("Responsibility and authority of the pilot in command") says that:


  The pilot in command of an aircraft is directly responsible for, and
  is the final authority as to, the operation of that aircraft.


When an aircraft is operating as Air Force One, it would normally be flown by the designated high ranking USAF Officer, as a military flight.

Is the President, as Commander in Chief of the armed forces, able to over-ride the authority of the pilot? 

For example, if one of the current Boeing VC-25's engines flames out and the captain announces that he has made the decision to take an option/ turn back - can the President override this decision and force him/her to continue the flight?
The pilot in command has final authority over Air Force One
Air Force Instruction 11-202, Volume 3 says the following in Chapter 1, part 1.1.1 (as in, the very first thing in the document):

1.1.1. Pilot  in  Command  Authority. The Pilot in Command (PIC), regardless  of rank, is responsible for, and is the final authority for the operation of the aircraft.

Just for fun, let's compare it to the civilian version that you referenced, 14 CFR 91.3:

The pilot in command of an aircraft is directly responsible for, and is the final authority as to, the operation of that aircraft.

Wow! Basically identical except that the military version goes out of its way to mention that rank is irrelevant.