In a small or medium mixing bowl, whisk the all-purpose flour, baking soda, and salt together. Set aside.
In a small saucepan, melt the butter over low heat until it’s completely liquified. Add it to another mixing bowl along with the granulated sugar and brown sugar.
Whisk the butter and sugars together for 1-2 minutes until everything is fully incorporated and slightly airy.
Add the soy milk (or another plant milk) and vanilla extract, then whisk the mixture again until it’s smooth.
Transfer the dry ingredients to the bowl of wet ingredients and stir together with a spatula until just combined.
Fold in the chocolate chips, then cover the bowl and chill it in the fridge for at least 4-6 hours but preferably overnight.
Once the dough is chilled, preheat the oven to 350F and line 2 baking pans with parchment paper or a silicone baking mat.
Using a 2-tablespoon cookie scoop, form cookie dough balls and transfer them to the prepared baking pan, making sure to leave a few inches in between.
Bake the cookies for 10-12 minutes, or until the edges are just turning golden but the centers are still soft (the time varies slightly depending on each oven, so keep an eye on them after the 9-minute mark).
Remove the pan from the oven and smack it down a couple of times to flatten the cookies and create ripples. Sprinkle the tops immediately with flaky sea salt.