The top picks globally to counter Ekko include Kalista, Lucian, and Zeri. These picks are all good at countering Ekko with win rates over 54%. Even if these Ekko counter picks are not used in the same position as you, it's not smart to take him into any of these matchups. They will most often win against Ekko.
Yet, if the opposite team choses either Akshan or Zyra, Ekko mains should strongly think about taking him, as he easily dominates these champs with win rates over 53% against each ofthem.