Preheat the oven to 350 degrees. Line a standard size muffin tin with parchment paper liners. These liners are the best. They release easily every single time. They are worth it.
In a bowl of a stand mixer fitted with a paddle attachment, combine the pumpkin, vinegar, applesauce, oil, almond milk, and sugars. Mix on low for one minute. Then, increase speed to medium and mix for an additional minute until the ingredients are well combined. Scrape down the sides of the bowl as needed.
Next, add in all of the remaining dry ingredients, except the chocolate chips.
Mix all of the ingredients together until just combined. Fold in the chocolate chips.
Fill each muffin nearly to the top
To make the crumb topping, place the flours, sugar, and cocoa into a bowl. Whisk together. Pour the oil into the bowl and work the oil into the dry ingredients using a fork. The crumbs will be sandy in texture and dark in color.
Distribute 1 tablespoon of the crumb mixture over each muffin. Very gently press down a slight bit. Place 4-5 chocolate chips onto the top of each muffin.
Bake for 25-30 minutes or until the center is set when a cake tester is inserted into the middle.
Allow the muffins to cool in the pan for 10 minutes before removing to a cooling rack. Allow the muffins to sit for 30 minutes before serving.