Preheat the oven to 425 degrees Fahrenheit/220 degrees Celsius. Spray the muffin pans with cooking spray or oil them or line with cupcake or muffin liners.
Zest the oranges. Then peel the oranges and puree in a blender or food processor into a coarse puree. Make sure there are no seeds. Reserve the zest and puree.
Place all the dry ingredients in a large bowl--flour, baking powder, baking soda and salt. Whisk until well blended.
Stir in the sugar, then add the orange zest, puree, vinegar, yogurt, milk, sugar and vanilla.
Mix using a spatula or a whisk but don't overmix. Just mix until everything is incorporated and there is no dry flour, especially at the bottom of the bowl.
Stir in the chocolate chips and mix them in.
Scoop out the muffin batter into the prepared muffin pans.
If you reserved some chocolate chips for the muffin tops sprinkle them now. You can also sprinkle some sugar, as I did, which gives a really nice, crackly top, but you can skip this, especially if you used the full cup of sugar in the recipe.
Bake in the preheated oven for 10 minutes, then lower the oven temperature to 375 degrees and bake for 18 more minutes or until a toothpick inserted in the center of a muffin comes out dry or with crumbs sticking to it.
Let the muffin tin cool for 10 minutes, then gently lift out the muffins. Eat warm or cold.