They sentenced me to twenty years of boredom
For tryin' to change the system from within
I'm coming now, I'm coming to reward them
First we take Manhattan, then we take Berlin
I'm guided by a signal in the heavens
I'm guided by this birthmark on my skin
I'm guided by the beauty of our weapons
Leonard Cohen is drawing a parallel here between Berlin and Manhattan, and since he’s writing about “taking” Berlin, we can assume he means the communist East (as it was back then). 
 He’s suggesting that control systems are in place in Manhattan that are very different, but just as effective, strict (and restrictive) as those of Berlin, e.g. the near-fascistic nature of the fashion industry (you must be wearing this season’s trends, you must be a size zero, you must have this particular facial bone structure this year); the increasingly pernicious influence of mass media, and the gradual but inevitable appearance and growth of totalitarian traits in our governments as they take ever bolder strides towards the right. 
 In short, although we in the west consider ourselves enlightened and free, we are subject to the same levels of control as somewhere like East Berlin. These control systems are just as strong (albeit at differing degrees of subtlety depending on our individual levels of intelligence and perceptiveness – but you can be sure that they’re there) and just as effective – if not more so, for many of us are made to be “happy in our servitude”. 
 So before we go looking to free others, first we must free ourselves, or else we will simply free others into a more elaborate and less visible prison.
First We Take Manhattan