Who has final authority over Air Force One?
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.