Preheat the oven to 350°F (175°C) and line a 9-cup muffin pan with muffin papers.
In a small bowl, combine 2 Tbsp ground flax seed and 6 Tbsp water; stir and let sit 10 minutes until thickened to a gel-like "flax egg", stirring occasionally.
In a mixing bowl, mash the 3 peeled ripe bananas with a fork or masher, then whisk in the flax egg and 2 tsp vanilla until combined (some banana chunks are fine).
In a separate bowl, whisk together 2 cups super fine almond flour, 5 Tbsp tapioca flour, 1 Tbsp ground cinnamon, 1 tsp baking powder, and 1/2 tsp sea salt until evenly mixed.
Pour the dry ingredients into the wet banana mixture and stir gently until just combined.
Fold in 2/3 cup vegan chocolate chips, reserving a few to sprinkle on top if desired.
Spoon the batter into the prepared muffin cups, filling each about three-quarters full.
Bake on the center rack for 28 to 35 minutes, until muffins are set and lightly golden at the edges.
Let the muffins cool in the pan at least 30 minutes before removing the papers and serving.