Countering Empoleon using Cloyster is hard, there is no way around it.
On the standard Cloyster set (Shell Smash + SKill Link) the best thing it can do is score a 3HKO after a Shell Smash with Rock Blast.
>+2 252+ Atk Cloyster Rock Blast (5 hits) vs. 252 HP / 0 Def Empoleon: 135-160 (36.2 - 43%) -- approx. 99% chance to 3HKO after Leftovers recovery
As the other answers have said, there is HP Ground/Electric/Fighting and Mud Shot, but they really aren't viable, and there is no point having a max Special Attack Cloyster just to use them, as it won't be able to deal with much besides Empoleon.
Your best bet is to try to deal with Empoleon before sending Cloyster out. If you don't have a good Empoleon counter on your team, and it is proving to be a large problem for you, then you should probably get one. Any Special Electric or Fighting type should do the trick - Pokemon like Galvantula, Special Lucario, or Mega Ampharos can usually deal with it. Special Attackers are better because they don't care if Scald burns them. On the other hand, Empoleons are usually Specially Defensive for this very reason, but it is a trade-off.
Since I don't know your team, then I can't say whether you should get rid of Cloyster, or if you should get rid of something else on your team,
Personally, I don't find Empoleon to be much of a problem because they usually run a supportive move set, with Stealth Rocks, Roar, Scald, and a coverage move like Flash Cannon or Ice Beam. Since they aren't used as sweepers, they don't usually take out a lot of your Pokemon. But, of course, if it is Cloyster vs Empoleon as the only Pokemon left, then Empoleon is pretty guaranteed to win.