Preheat oven to 375 degrees (F). Line a large baking sheet with parchment paper; set aside.
In the bowl of a stand mixer fitted with the paddle attachment, or in a large bowl using a handheld electric mixer, beat the coconut oil, both sugars, and vanilla on medium-speed until smooth; about 2 minutes. Add in the molasses, coconut milk and pumpkin puree and beat on low speed until well combined. Turn mixer off.
In a separate bowl combine the flour, baking soda, salt, and pumpkin pie spice; whisk well to combine.
Add the dry ingredients into the wet mixture and, with the mixer on low speed, beat until ingredients are combined. The batter will be very thick! Fold in 1 and 1/4 cups of the chocolate chips.
Scoop three tablespoon sized mounds of dough onto the prepared cookie sheet, leaving a few inches between each cookie. Bake for 9 to 10 minutes, or until the edges are golden and the centers are soft but set. Press remaining chocolate chips on top of warm cookies, and sprinkle with sea salt, if using. Cool cookies on the baking sheet for 30 minutes before transferring them to a cooling rack.