If using fresh clams, shuck them over a bowl to catch their juices. Measure 2 cups of juices, transfer to a small saucepan and heat just to boiling. Meanwhile, in a soup pot heat butter over medium-high heat, add leeks, celery and pepper and saute, stirring, for 10 minutes, without browning. Reduce heat and whisk in flour. Cook, stirring constantly, for 2 minutes. Whisk in boiling clam juice and fish or chicken stock and heat to simmering. Add potatoes. Squeeze tomatoes with your hands into soup pot. Stir in thyme leaves. Simmer for 20 minutes.
In a food processor blend 2/3 cup of clams to a puree; coarsely chop remaining 1 1/3 cups clams. When ready to serve, reduce soup to barely simmering and vigorously stir in pureed clams. In a small saucepan combine coarsely-chopped clams with a ladleful of chowder and heat for 20 seconds over low heat. Divide chowder among soup bowls and top each portion with some chopped clams. Garnish with thyme sprigs.