Mix ground flax seed with water in a large mixing bowl and let that sit for a couple minutes to thicken. While that thickens, preheat the oven to 350F and line 12 slots of muffin tin with muffin liners
Pour pumpkin puree, greek yogurt and maple syrup into the bowl with the flask and whisk to combine thoroughly.
In a separate bowl, mix together whole wheat flour, pumpkin pie spice, baking soda, baking powder and kosher salt. Pour dry ingredients into wet and fold in with a flat spatula.
Fold in chocolate chips with a flat spatula.
Scoop ¼ cup of batter into each of 12 muffin cups. Top with extra chocolate chips and bake at 350F for 25 minutes.