Preheat the oven to 350°F. Line a muffin tin with cupcake liners and set aside.
In a medium bowl, stir together the flour, baking soda, baking powder, salt and cinnamon. Set aside.
Add the ginger and sugar to a separate mixing bowl and massage together between your fingertips. Using a hand or stand mixer fitted with the paddle attachment, mix the butter and granulated sugar mixture together until light and fluffy, 2 to 3 minutes.
Add the eggs, one at time, mixing until combined. Add the molasses and mix until blended. It is okay if the batter is a little curdled.
Stop the mixer and scrape down the bowl. Add in half of the flour mixture and stir to combine. Pour the sour cream and water into the batter and mix to combine. Add the remaining flour and stir until the batter is smooth and evenly combined.
Fill the cupcakes liners so that they are about ¾ full with batter. You should be able to make 16 cupcakes. Bake for 20 to 22 minutes or until a toothpick inserted into the center of the cupcake comes out clean or with a few moist crumbs. Cool the cupcakes on a wire rack before adding any frosting.