Preheat oven to 350 degrees F. Line a couple of cookie sheets with parchment. If you aren't planning to bake any cookies right away there's no need to preheat.
Sift or thoroughly whisk together flour and baking soda and salt. Set aside.
Cream butter and both sugars with an electric mixer; Add egg, miso and vanilla and beat until blended.
Add flour mixture and stir until incorporated. Stir in chocolate chips.
Use a medium size cookie scoop to portion out dough. If chilling, put the dough portions on dinner plates lined with plastic wrap and cover. I recommend baking a few dough balls immediately and chilling the rest.
When ready to bake, space about 2 ½ inches apart on a Silpat or parchment lined baking sheet. Sprinkle tops of cookies with a few flakes of sea salt. Bake one sheet at a time, rotating halfway through, for about 13 or 14 minutes.
Let cool on the baking sheet for about 3 minutes, then carefully transfer to a wire rack to finish cooling.