In a large bowl, whisk together flours, baking soda, baking powder, and salt. Set aside.
Using a stand mixer fitted with the paddle attachment, cream butter and sugars together until very light, about 5 minutes. Add the eggs one at a time, mixing well after each addition. Mix in the vanilla. Reduce the speed to low, add the dry ingredients, and mix until just combined, 5 to 10 seconds. Use a wooden spoon or rubber spatula to fold in chocolate chips.
At the point you can bake the cookies or press plastic wrap against the dough and refrigerate it for 24 to 72 hours.
When you're ready to bake the cookies, preheat the oven to 350ºF. Line a baking sheet with parchment or a Silpat. Scoop generous mounds of dough onto the baking sheet. Sprinkle lightly with sea salt and bake until golden brown but still soft, 18 to 20 minutes. Transfer the sheet to a wire rack for 10 minutes, then transfer the cookies to another rack to cool completely. Repeat with the remaining dough.