Position the racks in the lower and upper thirds of the over and preheat the oven to 350 degrees. Line two baking sheets with parchment paper.

Sift together both flours, the baking soda, and salt into a medium bowl. Set aside.

In the bowl of the stand mixer fitted with the paddle attachment, cream together the butter and both sugars on medium speed for about 5 minutes, or until pale, light, and fluffy. Scrape down the sides and bottom of the bowl as necessary. Beat in the eggs and vanilla until thoroughly combined. Scrape down the bowl. Reduce the speed to low, add the dry ingredients, and mix until the flour is completely blended, scraping the bowl as necessary.

Remove the bowl from the mixer and fold in the chocolate chunks until evenly distributed. If you aren't baking the dough right away, you can refrigerate it now, well wrapped, for up to 1 week or freeze it for up to 1 month.

Drop the dough by heaping tablespoons, 2 inches apart, onto the prepared pans. Flatten each cookie slightly. Bake for 15 minutes or until golden, rotating the pans halfway through baking. Transfer the cookies to a cooling rack to cool completely.