Soften the butter slightly by giving it 15 seconds or so in the microwave on high. Place the butter in a large bowl and add the granulated and brown sugars. Using an electric mixer on medium-high, cream the butter and sugars until light and creamy, 3-4 minutes. Add the eggs one at a time while mixing then add the vanilla extract. Add the flours, baking soda, baking powder and salt then mix on low until just uniform. Add the chocolate chips and mix on low until mixed in.
Use an 18-8 scooper to portion out the cookies and form each portion into a ball, about 2 1/4 inches in diameter. Place the cookie balls on a parchment covered baking sheet and freeze overnight. Remove the cookies from the baking sheet and place in a gallon Ziplock bag in the freezer until ready to bake.
To bake, preheat the oven to 350 F and place the desired number of cookies on a parchment lined baking sheet. Keep the cookies widely spaced, no more than six for a 12 x 18 inch baking sheet. Bake for 22-24 minutes until the centers look set and the edges are slightly brown. Remove from the oven and cool on the baking sheet for several minutes then remove to a cooling rack to cool completely.