Preheat oven to 400 degrees and spray 12 liner cups with cooking spray; set aside. In a large bowl, combine flours, baking powder, baking soda, and salt. In a separate bowl whisk eggs, yogurt, oil, milk, sugar, and vanilla. Add the dry ingredients to the wet and stir until everything is moistened (Do not over mix.) Fold in chocolate chips. Spoon teh abtter into the muffin cups, 2/3 full. Bake for 20-25 minutes or until golden brown and a toothpick inserted comes out clean. Cool for 10-15 minutes before removing from muffin tins.