In a medium bowl whisk together flour, baking soda, baking powder, salt, and spices. Set aside.
Place butter in a medium, heavy-bottomed saucepan over medium heat and melt. [optional: browning the butter will give more flavor to the cookies, but it's only optional. To brown the butter, keep heating the butter after it's melted just until small golden bits start to appear at the bottom, and the butter smells nutty and delicious. Watch it carefully because the butter can burn quickly at this point]. Remove from the heat and immediately pour melted butter into a large bowl. Add granulated sugar and brown sugar and whisk until well blended. Add pumpkin puree and vanilla extract and whisk until combined. Add flour mixture and fold just until blended. Don't overmix. Fold in chocolate chips. Chill the dough for 30-60 minutes in the refrigerator.
Once dough is chilled, roll dough into balls, the size of 1.5 tablespoons (30g) each, and place on prepared pans 2-inches apart. The cookies won’t spread much, if at all, during baking so flatten them to desired thickness before baking.
Bake for about 12 minutes or until cookies appear set and slightly brown at the edges. The cookies will look soft and that's ok. You don't want to overbake them to keep them soft and chewy. Allow cookies to cool for 10-15 minutes in the cookie sheet, then gently transfer them to a wire rack to cool completely. Serve cookies at room temperature.
Store cookies in an airtight container at room temperature for up to 2 days or in the refrigerator for up to 1 week. Cookies can also be frozen for up to 2 months. To thaw, leave them on the counter, still covered, or overnight in the fridge.