from the same page you linked:
Cracked: These stones bear an obvious crack, whether as a result of the crafting process, because the raw stone was already cracked, or because the stone has been damaged (for example, if it gains the broken quality). A cracked stone’s power is usually the same as an undamaged stone, but weaker.
Emphasis mine. So, simply using a stone that already has a crack in it as the crafting material would automatically make the end result a cracked Ioun Stone. If this is about lowering the cost of the crafting process, I am pretty sure the DM would allow you to simply buy a pre-cracked stone at a lower price - since this makes up a good portion of the crafting cost, you'd already save some money.
I am guessing that "whether as a result of the crafting process..." refers to getting a subpar result on the crafting check. IIRC, if you manage to make a check's DC with your crafting skill and roll, you can always choose to have the result of your check be lower than what you rolled, since that purposefully makes the item you create work worse than it should by your roll. I think you are also allowed to just forego the roll entirely and just take the result your skill bonus gives you in case of crafting - if you can make the DC regardless, because your skill bonus is high enough, some DMs actually allow this to speed up the game. And if your skill bonus just barely misses the DC, the DM might tell you that you actually cracked the stone while crafting, but still managed to craft it.
In any case, these suggestions are not exactly RAW. The exact process for crafting your Ioun Stone is up to your DM - the RAW are purposefully vague on this, because they want to promote creativity, since crafting powerful items may even become an entire sub- or sidequest, sending you on a hunt for rare materials - but I think you should be able to purposefully craft a cracked Ioun Stone. It would require asking the DM in any case, maybe he even allows you to lower the DC of the craft check to make a cracked stone, but there are no exact rules on that in the RAW, mind you.