Neither about Amsterdam I think, both are quite big and surely now the one in Rotterdam is the biggest in Europe :3
Haven doesn't really mean the same as harbour or port, although it is in some place names (e.g. Milford Haven and various in the US east coast). If you just say 'the haven' people will look at you funny and assume that you are talking about a safe haven from something, not a harbour.
Technically it is correct but it wouldn't be understood as having that meaning without context. Haven in English is more often used in a non-watery sense. (native English speaker).