Preheat oven to 375°F / 190°C. Line a 12-cup muffin tin with paper liners.
In a small bowl, mix together the water and flaxseeds. Set aside to allow it to gel.
In a large bowl, mix together the flour, sugar baking powder, baking soda and salt. Make a well in it, and add in the milk alternative, oil, vinegar, and flax egg. Mix everything together using a fork, or a hand beater on low speed, until all the ingredients are just combined. The batter might seem a bit thick and gummy compared to non-vegan muffins that contain egg, but it's ok. Gently stir in the chocolate chips.
Evenly divide the batter into the muffin cups. Each muffin cup will be about ¾ full. Top a few muffins with additional chocolate chips if desired.
Bake in the oven for about 16-18 minutes, until a toothpick inserted in the middle comes out clean and the tops are a light golden brown.
Allow to slightly cool in the tin, then transfer to a wire rack to finish cooling. I love these muffins after they have fully cooled, including the chocolate chips. They are delicious the next day.