Police said Fowles, 58, will appear in custody at court on Monday. McGinn, 48, has been bailed and is due to appear at court on Jan.22.
A third man who was arrested along with the other two suspects was released, police said. He was not identified.
Police removed all passengers from the plane, but said a search found nothing suspicious aboard.
The arrests came amid heightened concern over airline security following an alleged Christmas Day attempt to blow up a Detroit-bound Northwest Airlines plane. In a separate incident Friday, fighter jets were launched to catch up with an AirTran Airways jet to San Francisco after a report that an intoxicated passenger had locked himself in a bathroom.
The Emirates flight, which had 331 passengers on board, was grounded in London overnight but had taken off Saturday afternoon.