13month old, allergies and 2 past ear infections who is falling all the time and hates standing or sitting in water. Could it be an ear problem?

Yes. Your child might have fluid in the middle ear - serous otitis media or otitis media with effusion. After an ear infection or during a cold or allergies, there may be residual fluid in the ear that is not infected. It may take time for this to go away. If the problem continues for more than a few weeks, it would help to have your pediatrician look in the ear again to ensure there is no infection.
13 MONTHS. Kids are examined all the time to find out the cause of the problem, unlike adults who can tell you what's wrong with them. Your kid will pull or point to his ears if it is painful at this age. Other causes of falling down is plumbism which is done by now. Perhaps he is not ready for the water yet. After pe you will know if he is fine.