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No. As I'm sure you know all S-Corp income taxes are passed through to you personally. You will get a credit for those taxes on your NYC personal income tax return and you will be able to deduct the payments made in 2015 as an Itemized deduction on your 2015 personal federal income tax return.
OK, you are talking about the NYC Corporate tax that treats S-Corps like regular corporation for NYC tax purposes.
So, yes they (NYC corporate estimated payments made by the S-Corp.) would be deductible as an expense on your 1120-S.
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