Sift flours, baking soda, baking powder and salt into a large bowl. Set aside.
In a separate bowl, cream butter and sugars together until very pale and light, about 5 minutes. Add eggs, one at a time, mixing well between additions. Stir in the vanilla.
Reduce mixer speed to low, add dry ingredients and mix until just combined, 5 to 10 seconds.
Stir in chocolate pieces without breaking them.
Press plastic wrap against dough chill in the refrigerator for 24-72 hours. Dough can be used all at once, or in batches.
To bake, preheat oven to 350 degrees Fahrenheit. Scoop 6 3 1/2-ounce mounds of dough (the size of generous golf balls) onto a parchment paper lined baking mat. Flatten out any chocolate pieces that are poking up; it will make for a more attractive cookie. Sprinkle lightly with sea salt. Repeat with remaining dough.
Bake until golden brown, but still soft, about 18 to 20 minutes. Transfer sheet to a wire rack for 10 minutes, then remove cookies to another rack to cool further. Best eaten warm.
No substitutions! Make sure you buy the high quality chocolate and specialty flours recommended in the recipe and chill the dough at least 24 hours (ideally 36) before baking.
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