1 cup (2 sticks) salted butter, at room temperature 3/4 cup packed dark brown sugar ¼ cup granulated sugar 2 large eggs, at room temperature 2 teaspoons pure vanilla extract 1½ cups dark rye flour 3/4 cups all-purpose flour ½ teaspoon baking soda ¼ teaspoon fine pink Himalayan salt 1½ cups chopped dark chocolate chunks or chips 1 cup mini pretzel twists, roughly crushed Flaky sea salt
1.Preheat the oven to 350°F. Line a haking sheet with parchment paper.
2.Melt 1/2 cup of the butter in a small saucepan over medium heat. Cook stirring, until the butter begins to brown, 3 to 4 minutes. Transfer the butter to a heatproof bowl and place the bowl in the freezer to chill for 10 to 15 minutes
3. In a large bowl, using an electric mixer, beat together the cooled brown butter, the remaining 1/2 cup butter, the brown sugar, and the granulated sugar on low, then slowly increase the speed to high and beat until fluffy about 2 minutes. Add the eggs, one at a time, beating until each is combined, about 1 minute per egg. Add the vanilla and beat until creamy, 1 minute more. Add both flours, the baking soda, and the salt, and beat until just combined. Fold in the chocolate chunks.
4.Roll the dough into 1-tablespoon balls. Arrange the balls on the prepared baking sheet, spacing them 2 inches apart. Gently press a few crushed pretzel pieces all over each dough ball, firmly sticking them in.
5.Bake the cookies for 7 minutes. Remove the baking sheet from the oven and tap it firmly against the counter a few times to fatten the cookies. Return to the oven and bake until the cookies are just beginning to set around the edges but are still doughy in the center, 1 to 3 minutes more. Remove the baking sheet from the oven and tap it firmly against the counter to flatten the cookies again. Sprinkle the cookies with flaky salt and let them cool on the baking sheet; they will continue to cook slightly. Enjoy the cookies warm or at room temperature, Store at room temperature in an airtight container for up to 4 days.