Mix chia seeds and almond milk. Let sit for at least an hour in the fridge. Add the rest of chocolate chia pudding ingredients. Mix in a high speed blender or Nutribullet.
Place a few cherries and some cacao nibs, if using, at the bottom of a 3 ounce bath cup. Then pour a little chia pudding on top. Place another couple of cherries on top of the pudding, then add more pudding on top. Repeat with the rest of the popsicles.
Put a popsicle stick into each one and freeze until solid. To get the paper cup to release easily, pour hot water into a shallow container and put popsicle in it. It should slide right off!