El Nino may affect many animals' habits, but proving that any changes were actually caused by El Nino is difficult. There are just too many factors to measure. We don't know for certain what triggers whales to migrate.
Some scientists theorize that length of day is the most important cue.
Others think that changes in water temperature stimulate whales to migrate. Different species probably use different cues. This year, the numbers of gray whales migrating along the west coast of the U.S. are lower than normal. We could speculate that El Nino has affected this population, but we really don't know what has caused the decrease in numbers. I'm sorry that I could not give you a more positive answer.