For low carb, omit potatoes and flour. Allow to simmer and reduce for a bit longer to thicken.
To reduce the fat even more, use skim milk or milk alternative. Then to help thicken the soup, increase the amount of potatoes used, mashing some of them up against the side of the pot. Or you can add some pureed cauliflower to help thicken the chowder.
*Clam juice can be found in the juice aisle of most supermarkets (near the tomato juice)