The hosts gave the league leaders an early test when Tyrone Barnett found space before unleashing a shot with his right foot, which was saved by the Orient keeper.
Scott Cuthbert attempted to hit back for Orient in the 30th minute, but his headed effort was saved with ease.
However, just before the break Mooney produced a well-timed strike from the centre of the box to bring things level going into the break.
Orient produced some good attacking football after the break and took the lead when Cox crashed home a right-footed effort into the top left corner.
Having grabbed his side's equaliser, Mooney then popped up in the 58th minute to put his side further in front as he finished after being played in by previous goalscorer Cox.