I think cravings can be psychological (you associate X food with pleasure or some positive emotion, and therefore crave the food) or physical (your body needs something OR your body is jonesing for a substance that is physically addictive, like sugar).
You can also work at finding a healthier substitute for whatever craving the cookies satisfy.
Is it the flavor of chocolate? Then how about a chocolate-flavored herbal tea? Or just a bit of raw chocolate (
www.rawfoods.com or
www.eatraw.com carries it) in some rice or soy milk? That's what's I'd do, but other folks might just get chocolate soy milk or chocolate milk).
Is it the crunch of the cookies? Then how about a handful of nuts? (raw is best, as they contain enzymes the help with the digestion of their fat and protein). Or maybe a crunch fruit, like an apple, which can help with both the sweet craving and the crunchy craving. And the pectin (fiber) in the apple will help you feel satisfied.
(Loving to eat apples instead of cookies doesn't happen automatically! You have to make the choice to eat the apple instead of the cookie, until the apple is actually what you prefer.)
Also, what do YOU mean by 'cleaning up your eating"? If it includes avoiding carbohydrates, that could be a source of cravings for sweets (because your body is lacking glycogen). Try to incorporate fruits in your diet (if you are concerned about such things, stick with low-glycemic fruits like berries and apples and pears).
Also, since you know what your weakness is (cookies!), do as you intend and keep them out of the house. "Working on" keeping them out isn't cutting it, it seems, so you have to declare a moratorium on cookies in the house. When you feel a craving, bake some from scratch from a healthier recipe or even prepare the dough ahead of time so you can keep it in a roll in the freezer, and cut off what you need---limit yourself to 2 or 3 at a time. When you eat those cookies, savor them, eating slowly, and relishing every bite, givning your full attention to the cookies and not just mindlessly eating them while watching TV. That can make 1 or 2 cookies as satisfying as 6 that you scarf down without thinking.