In a heavy 4 to 6 quart pot, over medium heat, cook bacon until crisp, about 10 minutes. Remove bacon from pot and set aside to drain. Crumble bacon once cooled. Leave bacon fat in pot for sautéing.
Add butter, onion, garlic, 2 sprigs of thyme and bay leaf to the pot. Cook while stirring often to keep vegetables from sticking. In 6-8 minutes onions should be translucent.
In another pot, while veggies are cooking add potatoes to boiling, salted water and cook until tender- about 10 minutes. Drain and set aside keeping the potatoes warm.
Gradually sprinkle flour into pot with vegetables until a thick roux forms. Cook while stirring for five minutes until roux is cooked through.
Increase the heat to medium high and slowly pour in the clam juice.
Add the potatoes.
Add in the clams and their juice but only add 1/4 juice at a time so as not to thin out the chowder too much.
Pour in the half & half and season salt and pepper, stirring as chowder thickens- this should take about 5 minutes. Continue stirring until chowder is thick and creamy. Finally, add the bacon back in.
Discard the bay leaf before serving. Garnish with reserved thyme.