In a mixing bowl whisk together the white and brown sugars until combined. Add the butter and switch to a hand mixer to blend together thoroughly and form a paste.
To the mixture add the eggs, vanilla and molasses mixing again until just incorporated. Be sure to not over-mix.
Pour in the all purpose and wheat flours, baking soda, and salt, again beating on low speed with the hand mixer until combined.
Fold in the chocolate chips and make sure they are evenly placed throughout the batter.
Make about ¼ cup sized cookie dough balls and place on a parchment sheet covered baking sheet.
Place a few chocolate chips on top of each dough ball.
Cover in plastic wrap and refrigerate the dough balls for 30 minutes.
Preheat the oven to 300 degrees Fahrenheit.
Make sure the dough balls are at least 2 inches apart and bake for 15-17 minutes until the tops of the cookies have set.
They will be lightly browned, but be sure not to over-bake as each oven heats differently.
Let the cookies cool for 15 minutes on the baking sheet or on a wire rack.
Serve with cold milk and enjoy!