There are several ways to get these stones. The Thunder, Leaf, Fire, and Water Stones can be bought in Lumiose City, but there are still some ways to get the other stones.
One way is Secret Super Training. Once a Pokemon is fully EV-trained, they unlock harder levels of super training. Many of these levels will give away evolution stones as their ultimate prize. Unfortunately, Moon Stones are the most annoying of the ones to get, because it is the top prize in Drag Down Hydreigon, but you have an equal chance of getting a Sun Stone instead.
Depending on which Stone you are talking about, some Wild Pokemon might have a chance of holding it. In the case of the Moon Stone, Clefairy and Lunatone have a 5% chance to hold it in the wild. I think the Super Training is more reliable, though.
Super Training source