The IRS accepts any exchange rate that is used consistently. So if the bank used a different exchange rate then you should use that exchange rate to calculate the US dollars that you are being taxed on.
IRS guidance on exchange rates
I'm not clear from your question whether the $1000 was a fee taken by the bank or whether it was just the difference in the exchange rate. If it was a bank fee that they charged you then I'm afraid that that is not deductible on your US return. If it was just the difference in the exchange rate resulting in you receiving a thousand dollars less than you would have at the exchange rate you were using then adjusting the exchange rate on your return to match the bank's should solve the issue.
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