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Route 229, Solaceon Ruins (With Dowsing Machine), Sunyshore City
Hope I helped!
Source: http://www.serebii.net/itemdex/thunderstone.shtml and experience

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There's a thunderstone on the southeast side of Sunnyshore City near a rock (the munchlax one I think)
Also theres one in Solaceon Ruins, or you can go into the underground and spend the next couple hours looking for one. =)

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