Melt 3 tablespoons of the butter in a large saucepan. Add the onion and cook until soft. Stir in the flour and cook about 2 minutes, stirring constantly. Slowly pour in the clam juice and cream. Season with salt, pepper and cayenne. Cook, stirring, about 3 minutes.
In another saucepan, melt the remaining 3 tablespoons butter. Add the shrimp and cook about 2 minutes. Add the crabmeat and cook about 1 minute. Stir into cream mixture.