Watch birds, sharks and 'cudas!
Sea gulls, pelicans and herons fly low over the flats and will often cause bonefish to spook or at least create a detectable, if subtle, dab of nervous water. Even a slight shudder can betray the presence of a bonefish and help you immensely by focusing your attention on a particular spot.
An osprey will actually take you right to the fish. Osprey will often hover over a school and will almost always cause bonefish to spook a bit giving you a welcomed shudder of nervous water.
Also watch sharks and 'cudas. They both push bones and also give you a clue as to their location. Even a small shark will cause bonefish to move out of the way.