I love them both but they are completely different. If you are in New England, they serve the New England style of course but it is better than anything you can get anywhere else. Lots of clams and cream, butter etc.
Whereas with Manhattan all I know is Campbell's, but I like it quite a lot too. So no choice possible. Bring me both.
New England Clam Chowdah is the only one! The other is a clam and tomato soup masquerading as a chowder.
(Oh and you need oyster crackers to go with the Chowdah)