Whisk the almond milk and ground flax seeds together in a medium bowl. Set aside for at least 10 minutes to thicken.
Preheat the waffle iron. Meanwhile, put the almond flour in a medium bowl and break up any lumps with your fingertips. Sift in the oat flour, millet flour, brown rice flour, and baking powder and whisk to combine; set aside. Whisk the flax mixture again, add the bananas or squash, oil, vanilla, and vinegar, and stir well. Add the flour mixture and stir with a rubber spatula until just combined.
Lightly brush the waffle iron with oil and scoop about a scant 1⁄2 cup batter (the exact amount will depend on your iron) onto the iron. Cook according to the manufacturer’s instructions, or slightly longer, until golden; vegan waffles usually need to cook for a few minutes longer than suggested for regular waffles. Remove the waffles and serve immediately with your choice of toppings, or place on a rack to cool if you are making them ahead. Repeat with the remaining batter. To store, once the waffles are cool, transfer to airtight containers and refrigerate for up to 3 days or freeze for up to 3 months.
Note: If you want to make and serve these waffles all at once, you can keep the first batches warm in a 200°F.