I would say that a certain level of TCP retransmissions and duplicate acks are expected, especially over the internet with multiple routing paths and non-reliable delivery.
Of course, we do not want to see too high a proportion of these! What overall rate of retransmissions do you have in this tcp stream?
Adjusting the window size would need to be done on both end-points - this would effectively increase the data pipe between the hosts before they require acknowledgement so in effect you would be able to increase the tcp throughput. I'm not sure if this is a good idea over the internet however, as reliability is never guaranteed so you could see more lost acknowledgements but for larger windows, hence higher payload retransmissions required and degraded performance.
But you'll never know till you try!
Kind regards, Ash.