Place the vegan butter, peanut butter and sugar in a mixing bowl. Using a stand mixer or regular mixer, mix on medium speed until creamy, about 2 minutes. Add the applesauce, milk, vinegar, and vanilla and mix until combined.
In a separate bowl, add the flours, cream of tartar, baking soda and salt. Stir until combined.
Add dry ingredients to wet ingredients. Mix well. Refrigerate the dough for 30 minutes. (see note for a faster way to do this)
Heat your oven to 350F. Get out a cookie sheet.
Shape the dough into balls slightly smaller than a golf ball.
Pour the sugar and cinnamon together in a bowl.
Roll cookie dough balls in cinnamon sugar until well-coated.
Place on cookie sheet approximately 2 inches apart.
Bake for 8-10 minutes. Remove from oven and allow to cool for a minute or two on the cookie sheet before transferring to an wire rack to cool completely.
Pour chocolate chips into a microwave-safe bowl. Add the coconut oil. Microwave the chocolate in 30 second increments, stirring in between until the chocolate chips are melted.
Use a spoon to spread melted chocolate over half of the top of each cookie. I like a nice, thick layer of chocolate. Then set aside to allow the chocolate to firm up. If you'd like to hasten this process, you could put them on a tray and store them in the fridge.