In Pokémon X and Y you can get a Thunderstone on Route 10, Route 11 and on Super Secret Training on the Follow Those Fleeing Goals regimen and The Battle for the Best: Version X/ Y regimen. Note you will not always get a Thunderstone on Super Secret Training.
You can also randomly get three Thunderstones from the Psychic Inver after an Inverse Battle. Note you will not always get the Thunderstones every time.
For more help getting a Thunderstone click on this video for the Thunderstone on Route 10 and this video for the Thunderstone on Route 11.
Hope I helped :)