Who's in charge on Air Force 1/Marine 1? POTUS? Pilot? Secret Service?

I would imagine it works like the majority of the armed forces. If someone is attached to you, they may be a higher pay grade, but fall under your authority.

If an E-4 is the stick leader on patrol, and they get an E-6 attached for any purpose, the E-4 is still the one who owns and runs the patrol.

Better yet, if there is an armed escort for a General, the ncoic, sncoic or oic has the final say. That oic is the subject matter expert not the General.

So if a Colonel is piloting for the president, the Colonel is the subject matter expert for the flight, not the president.

The pilot is in command of the aircraft (that is why they are officers) and all that pertains to flying that aircraft. The POTUS can tell the aircraft commander where to go, but not how to do it.

The aircraft commander or PIC is in command while the aircraft is on operation. For VIP/SAM airlift, this is from engine start to engine shutdown. There is typically a mission commander or mission liaison officer (who may be the Principal's executive or chief of staff) who can give direction on the mission or changes to the mission, but safety-of-flight decisions remain with the PIC. This was reinforced following the 1996 CT-43 crash that killed Sec. Ron Brown.