The MCTMT is defined, by NYS, as "a tax imposed on certain employers and self-employed individuals engaging in business within the metropolitan commuter transportation district (MCTD)". Some employers (depending on amount of payroll), including partnerships,, must pay MCTMT on their employees, this is generally done through your business.
Self-employed individuals and partners that over $50k in Self Employment income must also pay the MCTMT. If you have to pay the MCTMT, you have to pay quarterly with your other state estimated taxes on form IT-2105.
Whether or not your personal MCTMT taxes paid are deductible on your federal tax return is a question for accountants and lawyers. To me, deducting on Schedule C or K-1 doesn't make sense since the self-employment portion of the MCTMT is a personal tax, not a business tax.
How about deducting it on 1040 Schedule A? The IRS, in their instructions for schedule A line 5, say that you cannot deduct "Certain state and local taxes, including tax on gasoline, car inspection fees, assessments for sidewalks or other improvements to your property, tax you paid for someone else, and license fees (for example, marriage, driver's, and pet)." While this leaves an opening for them to reject the MCTMT, truth is, it doesn't matter much. For most people, the deduction would make a nominal difference to your federal taxes, and will likely be be reduced or eliminated in 2018 anyway.
However, most importantly, you cannot put your MCTMT estimated taxes into Schedule A using TurboTax. If you do, you'll essentially be claiming those estimated taxes twice.
1. They'll show up in your MCTMT wkst, and be credited against the MCTMT you owe.
2. They'll show up again in IT-201 line 75 (estimated tax payments) which flows from Schedule A.
