The top champs globally to counter Ekko include Kalista, Lucian, and Zeri. These champions are all great at countering Ekko with win rates over 54%. Even if these Ekko counter picks are not used opposite your position, it's not smart to choose him into one of these matchups. They will most often beat Ekko.
Conversely, if the opposing team brings either Akshan or Zyra, you should strongly consider picking him, as he easily wins against these selections with win rates over 53% against both ofthem.