Position a rack in the center of the oven and preheat to 350 degrees F. Line your baking sheet with parchment paper.
In a medium bowl, mix together flour, baking soda and salt. Set aside.
In a large bowl, beat butter and sugar using a mixer on medium-high speed until light and fluffy (about 2-3 minutes). Add eggs and beat until blended, then mix in vanilla.
Add the flour mixture in the butter mixture and carefully mix until just combined. Then increase speed to high to pull dough together.
Add half of the dark chocolate pieces and beat on high for for a few seconds to mix in.
Drop cookie dough in large spoonfuls on your lined baking sheet. Top each cookie with one of the remaining dark chocolate pieces.
Bake until lightly browned on top, 10 to 12 minutes. Top with flaky sea salt as soon as the cookies come out of the oven. Cool on the pan on a rack for 1 minute, then transfer the cookies to the rack to cool completely.