Sift flours, baking soda, baking powder and salt into a bowl. Set aside.
Using a stand mixer fitted with paddle attachment, cream the butter and sugars together until very light, about 5 minutes. Add eggs, one at a time, mixing well after each addition. Stir in the vanilla. Reduce speed to low, add dry ingredients and mix until just combined, for about 5 -10 seconds. Drop chocolate morsels in and incorporate them without breaking 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.
When ready to bake, preheat oven to 350 degrees. Line a baking sheet with parchment paper or a nonstick baking mat.
Scoop 6 3 1/2-ounce mounds of dough (the size of generous golf balls) onto baking sheet, making sure to turn horizontally any chocolate pieces that are poking up (if you used the disks); it will make for a more attractive cookie. Sprinkle lightly with sea salt and bake until golden brown but still soft, about 17 to 20 minutes (depending on how large or small your cookie dough balls are).