[Pseudoscience-is-malarkey (OP)]

Is what caused her twin-engine Lockheed Electra to crash most likely bad navigation when negotiating the unpredictable ocean waters? Aviation was still in its infancy in 1937.

[alancalverd]

Hardly infancy. The first flight from England  to Australia was in 1919, by which time at least one war had been fought with fighters and bombers.

Nothing particularly unpredictable about the Pacific ocean (essentially, buggerall chance of survival if you hit it in any kind of  airplane) but it is VERY BIG so a small headwind can result in ending up hundreds of miles short of your planned destination even if you were pointing in the right direction. Also VERY EMPTY so little chance of getting a credible enroute weather report even if your surface station radio is working. And

Earhart's transmissions seemed to indicate she and Noonan believed they had reached Howland's charted position, which was incorrect by about five nautical miles (10 km).

So their navigation may have been perfect but the chart was wrong, and they were certainly short of fuel at the time of their last known radio contact, when they said they were tracking north and south at 1000 ft in scattered low cloud looking for Howland island.