Preheat the oven to 350ºF. Line a muffin pan with paper liners.
In a large bowl, mix together the flours, baking powder, baking soda, salt, cinnamon, ginger and nutmeg. Set aside.
In a separate bowl, cream together the butter, sugar and vanilla until light and fluffy. Add the eggs, one at a time, then add the pumpkin and mix until fully combined.
Alternately add the dry ingredients and water to the flour mixture until fully incorporated.
Fold in 1 cup of the chocolate chips then fill the muffin cups about 2/3 full. Sprinkle the tops of the batter with the remaining 1/4 cup of chocolate chips then bake the muffins for 18-20 minutes or until a toothpick inserted comes out clean. Allow the muffins to cool in the pan for 5 minutes then transfer them to a rack to cool completely.