In a small bowl, stir together the chia seeds and water, and set aside. It will thicken while you prepare the rest of the dough.
In a large bowl, beat together the margarine, brown sugar, sugar, vanilla, and almond milk until smooth. Add in the soaked chia seed mixture, and stir until combined. Add in the flour, baking soda, and salt, and beat until completely incorporated. The dough will be fairly soft. Fold in the mini chocolate chips.
Cover the bowl, and refrigerate for 30 minutes to 1 hour. Preheat your oven to 375 degrees, and line two baking sheets with parchment paper.
Scoop the batter in two-tablespoonfuls onto your baking sheets. Bake for 10-12 minutes, or until the edges just start to become golden brown. Cool and enjoy!