This recipe dates back to the days of New York's famed Delmonico's in the late 19th century, and it remains to be a favorite recipe for many. In the recipe intro, he points out people tend to either like or hate Manhattan-style clam chowder. But he explains that the tomatoes are a great addition to clam chowder because they temper the salty broth and offer a pleasant sweetness that you won't find in most milk- or cream-based clam chowder recipes.
Put the clams in a large, heavy Dutch oven, and add about 4 cups water, then set over medium-high heat. Cover, and cook until clams have opened, approximately 10 to 15 minutes. (Clams that fail to open after 15 to 20 minutes should be discarded.) Strain clam broth through a sieve lined with cheesecloth or doubled-up paper towels, save the hot broth and set aside. Remove clams from shells, and set those aside as well.
Rinse out the pot, and return it to stove. Add butter, and turn heat to medium-low. Add bacon and cook, stirring occasionally, until the fat has rendered and the pork has started to brown, approximately 5 to 7 minutes. Use a slotted spoon to remove pork from fat, and set aside.
Add onions, garlic, celery, green peppers and carrots to the fat, and cook, stirring frequently, until the vegetables are soft but not brown, approximately 10 to 15 minutes. Season as desired with red pepper flakes (use sparingly, as the heat increases a bit over time.) Stir in potatoes, and continue cooking until they have just started to soften, approximately 5 to 7 minutes. Add 4 cups of clam broth, reserving the rest for another use. Add the sprigs of thyme and the bay leaf.
Partly cover the pot, and simmer gently until potatoes are tender, approximately 10 to 15 minutes. Using the back of a wooden spoon, smash a few potatoes against the side of the pot to release their starch and help thicken the broth.
Meanwhile, chop the clams into bits that are about the size of the bacon dice.
When potatoes are tender, stir in tomatoes, and heat them through. Add chopped clams and reserved bacon, stirring to combine. Add black pepper to taste. Let chowder come to a simmer, and remove from heat. Remove thyme sprigs and the bay leaf, and discard.
The chowder should be allowed to sit for a while to cure. Reheat it before serving, then garnish with chopped parsley. Serve with oyster crackers.