I'm quite sure this song is about the influence of the global Jewish banking industry. "First we take Manhattan" is a reference to the centre of international banking on Wall Street, and "then we take Berlin" is a vision of revenge against what the Nazis did to the Jews, by returning to the German capital and controlling the German economy by the capitalist banking system of credit and debt.
Other likely Jewish references contained in the song are "the signal in the heavens" referring to the Jewish idea of being God's 'Chosen People' and the "birthmark on my skin" which could refer to the Jewish mark of circumcision.
The key verse of:
"You loved me as a loser, but now you're worried that I just might win.
You know the way to stop me but you don't have the discipline"
is a beautiful juxtaposition of Cohen's hurt at what has been done to the Jews, plus his pride at the power the Jewish bankers now wield, but also tinged with the regret that maybe their economic supremacy is wrong and should be stopped, if only people had the "discipline" to do it. I saw him sing this song live in concert recently, and to see the feeling he puts into this line sends a shiver down your spine.
Like all Leonard Cohen songs, there is probably a parallel personal meaning about a relationship he was having with a woman at the time. But as far as general worldly meanings go, this song is certainly referencing the Jewish banking question.