Sift flours, baking soda, baking powder and salt into a bowl. Set aside.
Using a mixer fitted with paddle attachment, cream butter and sugars together until very light and fluffy, about 5 minutes. Add eggs, one at a time, mixing well after each addition. Stir in the vanilla.
Reduce the speed to low, and add dry ingredients and mix until just combined, 5 to 10 seconds.
Add the chocolate pieces and fold them inot the batter being careful not to break them. Press plastic wrap against dough and refrigerate for 24 to 36 hours. Dough may be used in batches, and can be refrigerated for up to 72 hours.
Move the oven rack to the middle position and preheat oven to 350°F. While the oven preheats, take the dough out of the refrigerator. Line a baking sheet with parchment paper or a nonstick baking mat. Set aside.
Scoop mounds of dough the size of generous golf balls (or use a #16, 4 Tablespoon scoop) onto baking sheet, leaving 2 1/2-3 inches between mounds. Sprinkle lightly with sea salt.
Bake one cookie sheet at a time until cookies are golden brown but still soft, 18 to 20 minutes. Transfer sheet to a wire rack for 10 minutes, then slip cookies onto another rack to cool a bit more. Repeat with remaining dough.