Heat oven to 375°F and line 12 muffin cups with paper liners or spray with baking spray.
Pulse 1/2 cup of the pumpkin seeds in a food processor until finely ground, but not a paste. Coarsely chop remaining 1/4 cup of the pumpkin seeds and set aside for the topping.
Combine ground pumpkin seeds with the 1 1/2 cups flour, 2 teaspoons baking powder, 1/4 teaspoon cream of tartar, 1/4 teaspoon kosher salt, and 2 teaspoons of the cinnamon in a medium bowl and whisk to break up any big lumps. Save remaining 1 teaspoon cinnamon for the topping.
Combine the 3/4 cup milk and 1/2 teaspoon cider vinegar in a large bowl and whisk to combine. Add the 2 eggs, 1/2 cup dark brown sugar, 1/2 cup pumpkin seed oil, 1/3 cup honey, and teaspoon vanilla and whisk until smooth. Add dry ingredients and gently fold in until just moistened, don't over mix.
Scoop batter into the prepared muffin pan using a cookie scoop if you have one.
In a small bowl combine the chopped pumpkin seeds, remaining teaspoon of cinnamon, and the coarse sugar. Generously sprinkle this mixture over the top of each muffin. Use all the topping.
Bake 20-25 minutes or until a toothpick inserted in the middle comes out with a few moist crumbs. Let cool at least 15 minutes then serve warm or cool completely, cover, and keep at room temperature for up to 2 days.