1. Preheat oven to 375ºF. Line a 12-cup muffin tin with paper liners or mist with cooking spray.
2. In a large bowl, whisk both flours, brown sugar, baking powder, baking soda and salt. In a medium bowl whisk pumpkin, eggs, yogurt and oil. Stir pumpkin mixture into flour mixture until just moistened. Stir in chocolate chips and 1/4 cup ginger.
3. Divide batter among muffin cups. Sprinkle with remaining ginger and pumpkin seeds. Bake until muffins are golden and a toothpick inserted into center of a muffin comes out clean, 20 to 22 minutes. Let cool in pan 5 minutes, then turn muffins out onto a rack to cool completely.