Whisk together 1 cup all purpose flour, 1 cup whole wheat flour, 3 tablespoons sugar, the 1/2 teaspoon baking soda, the 1 teaspoon baking powder, and the 1 teaspoon kosher salt in a large mixing bowl until combined.
Mash the 2 ripe bananas with a potato masher in a separate large mixing bowl then add the 1 1/2 cups milk, 1/4 cup oil, 3 eggs, and 1/2 teaspoon cider vinegar. Whisk until eggs are completely incorporated. Add wet mixture to dry mixture and stir with a rubber spatula just until moistened. Stir in the 1/2 cup chocolate chips.
Set batter aside and let rest for at least 10 minutes while the waffle iron heats up. Heat waffle iron according to the manufacturer's instructions. Spray the hot iron with cooking spray.
Ladle about 3/4 cup batter (or however much your waffle iron holds without overflowing) into the waffle iron and cook according to manufacturer's instructions. Repeat to cook remaining batter.
Serve waffles immediately with soft butter, warm maple syrup, sliced bananas, and extra chocolate chips, if desired.