In a large bowl or the bowl of a stand mixer fitted with the paddle attachment, cream the butter, Greek yogurt, coconut sugar, and granulated sugar with an electric mixer on medium speed until very light and fluffy, about 4 full minutes, stopping to scrape the bowl as needed. Add egg and vanilla. Beat until incorporated, scraping down the bowl as needed. The mixture will look curdled, which is just fine. Beat in the baking soda and salt until combined. Reduce the mixer speed to low and gradually add the white whole wheat flour, beating just until it disappears. The dough will look crumbly. By hand with a rubber spatula or wooden spoon, stir in the chocolate and mint chips. For the best flavor and to make sure the cookies are not too dry, refrigerate for at least 1 hour or overnight.
When ready to bake, place a rack in the center of your oven and preheat the oven to 350 degrees F. Line a baking sheet with parchment paper or a silicone baking mat. With a cookie scoop or spoon, portion the cookies by heaping tablespoons, spacing them 1 inch apart on the prepared baking sheet. Bake for 7 minutes, until barely dry on the top and edges but still gooey and soft inside. Let cool on the baking sheet for 5 minutes, then gently transfer to a cooling rack. (I like to slide my piece of parchment or silicone baking mat right off the baking sheet and onto the cooling rack.)
Dough can be prepared through Step 1 and stored covered in the refrigerator for up to 3 days or frozen for up to 3 months. Let stand at room temperature until soft enough to scoop, then bake as directed. (If frozen, thaw overnight in the refrigerator first.)
Scooped cookie balls can be refrigerated for up to 3 days or frozen for up to 3 months. To freeze, place the unbaked cookie balls on a baking sheet, freeze, then transfer to a ziptop bag. Bake directly from frozen, adding a minute or two to the baking time.
Baked cookies can be stored in an airtight container at room temperature for up to 4 days or frozen for up to 2 months.
You can bake the cookies right away without chilling, but the wheat flavor of the flour will be more pronounced, and they will taste a bit drier. Refrigerating allows the "wheat" taste to mellow and the dry ingredients to absorb moisture from the wet, resulting in a more perfect cookie. It's worth the wait!