Preheat your oven to 375F and line a baking sheet with parchment paper.
In a stand mixer with a paddle attachment, add your solid coconut oil and coconut sugar. Mix until combined then add in your maple syrup, vanilla, pumpkin puree, molasses, and non dairy milk. Mix for 1-2 minutes until combined.
In a separate bowl, add your flours, baking soda, salt, and pumpkin pie spice. Whisk together.
Add your dry ingredients to your wet ingredients in the stand mixer bowl and then mix until combined. Fold in your chocolate chips.
Scoop 1 ½-2 tablespoon sized balls of dough and place them on your baking sheet. This recipe makes about 16 cookies. Make sure to leave a few inches apart, the cookies won't spread too much, but they will a bit. Bake for 10 minutes, they will still be soft in the center but the edges and bottom will be golden. Once they're out of the oven, top with sea salt flakes.
Let them cool for 25-30 minutes then enjoy!
Storage: You can store them in an airtight container at room temperature for 2 days then move them to your fridge for an additional 4 days. You can store them in the freezer for up to 3 weeks and defrost in the fridge (though the taste will not be as great).