You can craft cookies with cocoa beans by putting cocoa beans in between 2 wheat in a crafting table.
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You cannot make cocoa beans. They spawn naturally in jungle biomes on jungle trees. You can also spawn them via creative mode. Hope this helps.
As of Beta 1.4, cocoa beans couldn't be found ingame. You can only find them inside dungeon chests. You can read more about dungeon chests on Minecraft Wiki (the link is under "Sources and related links" below this answer).
Cookies
Crafting Recipe: --------------- Wheat, Cocoa Beans, Wheat
You have to either find a brown sheep or Dye it with cocoa beans, which you can find them in chests or in jungles