Pour the warm water into the bowl of a standing mixer fitted with a bread hook. Sprinkle in the yeast and dark brown sugar. Let sit for 5 minutes.
Stir in the salt and canola oil and two cups of the flour. Add additional flour until a dough forms, about two more cups.
Knead the dough on a floured surface until the dough is smooth and elastic, several minutes. Turn the dough in a bowl greased with butter or oil, place in a cold oven, and let rise one hour.
Punch down the dough, briefly knead, and divide into 22 pieces.
Wrap each piece of dough around a piece of frozen cream cheese, pinching the dough to seal and rolling in your palms to form a ball. Place on a baking tray lined with parchment paper.
Preheat the oven to 450°F. In a large saucepan, pour the water, additional brown sugar, and the baking soda. Bring to a boil.
Using a slotted spoon, place several bagel balls into the boiling water at a time. Boil for 15 seconds, drain on the spoon, and return to the tray.
Bake until the bagels are golden brown and cooked through, 12 to 15 minutes.