Many people have have this question. After geomancy its almost unstoppable and before that it launches fairy aura boosted moonblasts which deals a lot of damage. Its a threat in both tiers.
Atleast tell its counter for one tier if you don't know its check for the other tier.
Thanks in Advance!
Countering Xerneas isn't much hard in Nat Dex AG. This is because:
Taking to Ubers. I don't play Ubers so I use Smogon's analysis. (For Gen 7 Ubers)
Necrozma-DM: Necrozma-DM has the defensive typing, ability, bulk, and moves needed to check most Xerneas sets. At best, Geomancy Xerneas can 2HKO support Necrozma-DM and avoid the OHKO from Sunsteel Strike; however, +1 Z-Geomancy Xerneas is still 3HKOed. Choice Scarf, Choice Specs, and the defensive set cannot do much to any Necrozma-DM variant.
Primal Groudon: Primal Groudon resists Moonblast, is always EVed to check boosted Xerneas, and can phaze Xerneas with Roar, afflict it with status, or smack it with Precipice Blades.
Magearna: Magearna tanks even any boosted attack from Xerneas well, and it removes said boosts with Heart Swap.
Defensive Steel-types: Klefki, Mega Scizor, Bronzong, and Aegislash can survive boosted attacks from Xerneas. They can inflict Xerneas with status or hit it hard with STAB Steel-type moves. Celesteela is defeated by Thunder and Ferrothorn is defeated by Focus Blast, but otherwise they can do the same.
Ho-Oh: Ho-Oh tanks Moonblast rather well and can hit Xerneas with strong physical attacks, inflict it with status, or phaze it with Whirlwind. However, Ho-Oh is incredibly vulnerable to Stealth Rock and is typically OHKOed by Hidden Power Rock.
Lugia: Lugia checks Xerneas via Multiscale and Whirlwind, but it is KOed by a boosted Thunder after Stealth Rock.
Blissey and Chansey: Both Blissey and Chansey can stall out most Xerneas sets with Toxic due to their powerful special bulk, but they cannot defeat Z-Geomancy Xerneas on their own.
Priority: Priority attacks are typically employed by offense teams and used to revenge kill a boosted Xerneas. Users include Extreme Killer Arceus, Mega Lucario, Marshadow, Deoxys-A, and Rayquaza.
Mega Gengar: Although not a check to boosted Geomancy sets, Mega Gengar can trap and eliminate the defensive set or revenge kill unboosted Geomancy and Choice Specs sets.
Arceus-Poison and -Steel: These Arceus formes have a Fairy-type resistance and are bulky enough to check most boosted Xerneas sets, but Arceus-Steel is KOed by +2 Focus Blast.
Hope this helps!