Battle Zapdos a second time (after you have beaten Rayquaza) then have Zapdos join the party. This allows access to the "Friend Area Legendary Island".

Head for Mount Blaze (Moltres) or Frosty Grotto (Articuno). You must be alone and you have to face off a L45 Zapdos, Moltres at L52 and Articuno at L53.