1.) Devoluter LA.
Yup. Devoluter. It's simple. It requires no Energy. And you can make a 130 HP Pokemon drop to 30 HP in one turn. Not only this, but if your opponent threw all his Magikarp into the discard pile, how is Gyarados going to attack? That's right. He can't.
Obviously I'll recover as if it was killed by regular damage, but they Gyarados is back in my hand. This would be a major threat if it wasn't stopped by Unown G, Gyarados wasn't generally 2-shot anyway and De-evoluter ends your turn and I'll just evolve again.
2.) Omastar MD.
I love this card. It's a universal Devoluter, and you can kiss Gyarados good-bye. It's quick, and it works just like Devoluter. Your opponent is less than likely playing any SP Pokemon in his or her Gyarados deck, so that ruins the possibility of a Power Spray. You're set with Omastar MD.
Correct me if I'm really wrong but I think that it doesn't de-evolve the active so you'd need to set up a stage 2 that suddenly becomes useless and get a Warp Point on the same turn all for one KO.
3.) Spiritomb PA.
Actually, this really isn't a counter. This is a follow-up card to Devoluter or Omastar MD. This locks your opponent from playing Night Maintenance in an attempt to bring any Magikarp or Gyarados back, or Super Scooping his Gyarados before you play the Devoluter.
This seems to be one of the reasons some people aren't playing Gyarados. I'll admit this hurts but only from decks that can truly abuse it (Uxie/Gliscor). Other decks that use it for setup don't keep it active every turn so the game proceeds normally after they're done setting up (the only Trainer I truly need is Pokemon Rescue and that's only after you're KOing me. I won't need Poke Turns to KO a Spiritomb. My list is also running a Palmer and I might make it two if I start seeing a lot of Spiritomb abuse decks. I can Sableye the Palmer, which gives you a prize but can Gliscor and Uxie KO 2 Gyarados before I get rid of their Spiritombs (and yes I'm running another 1-card counter for Gliscor lock).
4.) Skarmory FB SV.
Wow. I thought this card was terrible. But looking deeper, Skarmory FB can hold his own against Gyarados. Unfortunately, it's not very good late game: your opponent is set up, and he's probably done playing Magikarp so Silver Feather isn't very helpful. Early game, Skarmory FB is perfect. He drops two damage counters on every Basic Pokemon your opponent plays, leaving a Magikarp with 10 HP. Now, just do 10 more damage, and Devolute.
~Thanks to #1weavile with the counter.
Uh whut? Lol. No offense but this is the worst Gyarados counter I've ever seen. First of all, if I was going to lay a Magikarp down on the bench at all it would be because I was KO'd the previous turn. And Silver Feather only does 20 damage, so the chances of that are very unlikely considering I also have Super Scoop Up. Even if I were to be KO'd, I'd have to be the world's worst Gyarados player if I didn't evolve and free retreat my Crobat that turn to KO the Skarmory. If you ran Miasma I'd just drop my BTS counter. The only counter if Metagross and Skarmory but Skarmory still has to KO the Gyarados and that wouldn't be half good against anything else.
5.) Miasma Valley PT.
One of the better counters against Gyarados. If you play Miasma Valley from the get-go, you start layering down damage on your opponent's Benched Pokemon like there's no tomorrow. All the more damage to Devolute and KO. However, Miasma Valley PT is easily countered with a BTS in a Gyarados deck.
~Thanks to #1weavile with the counter.
You play Miasma and I play BTS when I need to lay anything down without getting damaged. I also generally have a bench of one evolved Pokemon for draw 1/3 games, the rest of the time my bench is basics. I'll just Unown G my Gyarados and then counter stadium when that gets KO'd.
6.) Mr. Mime MT.
Although this guy sits and stalls, he can prevent Gyarados from abusing you with Tail Revenge, he makes sure that your opponent uses the four to six Energy most Gyarados decks run. ...that's about as good as it's gonna get with Mr. Mime.
~Thanks to half the PokeBeach community with the counter.
You'd have to be up on prizes because generally decks with Mime don't seem to have Psychic Energy. Or you'd be Uxie/Gliscor. I'm also running eight energy in my list, three of which are Cyclone Energy. I can just give up a prize as I attach an energy. Then I Cyclone for a prize and take some damage then I attach the 3rd energy and KO. This seems to work 85% of the time I play Mime decks.