What does it mean if my baby’s eyes seem cloudy and watery?

Possible Cataract. There are other possibilities, but regardless of the cause, your baby needs to be seen by an opthomologist right away.
Blocked tear duct. If you are describing a intermittent mucousy film over the eye then it is probably a result of a blocked tear duct (lacrimal stenosis). The tears can't drain from the eye and secretions build up and sometimes get infected. If the cornea seems cloudy this may be a more serious problem requiring the attention of an ophthalmologist.