The first thing you have to understand is that any city or state income tax is based on where the income is earned for most employees. Where you live is not relevant unless you are a transportation worker which you are. If as a transportation worker you do not perform more than 50% of your work in a specific state you are taxed based on your residence. You should be able to file and get a refund on what you already paid.

“”Federal law provides that certain interstate transportation and commerce employees, such as pilots, are subject to tax in their state of residence and any state in which they earn more than 50 percent of their pay for being a pilot. This is determined by looking to whether the pilot’s flight time in any non-residence state exceeds 50 percent of the total flight time worked by the pilot while employed during the calendar year. The pilot may be entitled to a tax credit in his residence state for taxes on his pay that is paid to other states.””