Sift flours, baking soda, baking powder and salt into a medium sized bowl. Using a mixer fitted with paddle attachment, cream butter and sugars together until fluffy, about 3-4 minutes.
Add vanilla and eggs, one at a time, mixing well after each addition. Reduce speed to low, add dry ingredients and mix until just combined. Add chocolate chips and incorporate them by hand.
Press plastic wrap against dough and refrigerate for 1 hour. Dough can be refrigerated up to 48 hours if making ahead of time.
Preheat oven to 350° F (175C). Line a baking sheet with parchment paper. Roll cookie dough by hand into golf ball sized pieces; arrange on baking sheet with at least a 2″ space between cookies. Sprinkle lightly with sea salt and bake until golden brown and to desire level of doneness, 10-12 minutes for soft chewy cookies, 12-15 minutes for crisp cookies.
Cool cookies 10 minutes on baking sheet before removing. Repeat with remaining dough. Makes approximately 36 cookies.