Stones may be purchase in the Stone Emporium in Lumiose City. To get there quickly, take a cab and find this option. You can buy them for 2100 dollars or whatever the stupid currency is called.
In Super Training, you can play 3 games to obtain the stones by scoring the top score.
Score a Top Score in The Leaf Stone Cup Begins to get - Leaf Stone
Score a Top Score in The Fire Stone Cup Begins to get- Fire Stone
Score a Top Score in The Water Stone Cup Begins to get- Water Stone
Pretty easy to remember that.
Finally, there are spots that you can find these in:
Leaf Stone- Route 8
Fire Stone- Route 9
Water Stone- Route 8 and Route 12