Whisk together eggs, oil, yogurt or sour cream, vanilla and brown sugar until combined and smooth.
Stir in the zucchini, mixing just until combined with no large clumps of zucchini.
Add the white whole wheat flour, cocoa powder, salt, baking soda and baking powder, stirring just until combined. It is ok if there are some streaks of flour.
Fold in chocolate chunks or chips, saving about 1/3 of them to sprinkle on top before baking.
Fill muffin cups all the way to the top and sprinkle with remaining chocolate chips.