Combine flour, sugar, baking soda, and soda in a large mixing bowl. Pour in molasses and stir until partially incorporated.

Combine water, coconut oil, vinegar, and vanilla extract in a medium mixing bowl.

Preheat waffle iron on medium according to manufacturers' instructions. Grease both sides of the waffle iron.

Pour water mixture over flour mixture and stir thoroughly. Add chocolate chips. Ladle 1/4 cup batter into the waffle iron. Close and cook until browned on the outside, 2 to 3 minutes per waffle. Take out each waffle with a fork and place on a serving platter.