Sift flours, baking soda, baking powder and salt into a bowl. Set aside.
Cream butter, peanut butter, and sugars together.
Add vanilla and eggs one at a time, mixing well after each addition.
At a low speed add dry ingredients and mix until just combined, about 10 seconds.
Add chocolate chips and mix as little as possible to evenly distribute.
Chill dough if desired.
Scoop 6, 3 1/2 ounce (the size of a racket ball) onto baking sheet lined with parchment. Lightly sprinkle top with sea salt and bake at 350 for 15 to 20 minutes. Will spread to 5-6", so leave ample room. Cookies will still be soft, but beginning to brown.
Transfer sheet to a wire rack for 12 minutes to cool (DO NOT REMOVE COOKIES).