Combine flours, baking soda, baking powder, and salt in a bowl. Whisk well; then set aside. Using a mixer fitted with paddle attachment, cream butter and sugars until very light and fluffy, about 3 to 5 minutes.
Add the eggs, one at a time, mixing well after each addition. Mix in the vanilla. Scrape down the sides of the bowl with a rubber spatula as needed.
Reduce the mixer speed to low; then add dry ingredients, and mix until just combined. (Unless you have a plastic guard that sits around the rim of the bowl, this will make a big mess at first, with flour flying everywhere. I found that carefully holding a dish towel around the top of the bowl helped a lot.)
Add the chocolate chips, and mix briefly to incorporate. Press plastic wrap against the dough, and refrigerate for 24 to 36 hours. The dough may be used in batches, and can be refrigerated for up to 72 hours.
When you’re ready to bake, preheat oven to 350°F. Remove the bowl of dough from the refrigerator, and allow it to soften slightly. Line a baking sheet with parchment paper or a nonstick baking mat.
2 ways of baking these cookies:
Using a standard-size ice cream scoop, scoop six mounds of dough onto the baking sheet, making sure to space them evenly. Sprinkle lightly with sea salt, and bake until golden brown but still soft, 15 to 20 minutes.
OR roll the dough into 1 1/2 inch in diameter balls. You will be able to fit 12 on a tray. Sprinkle with sea salt and bake for 8 mins or so. Only until just browned on top.
Transfer the baking sheet to a wire rack for 10 minutes, then transfer the cookies onto the rack to cool a bit more.