Answer by Wray Rives:
is correct. Just because you register you LLC in one state does not mean that the LLC is not subject to taxes in other states as well. It is a commonly held misconception that you can register an LLC in a relatively low tax state and avoid taxes in higher tax states, but all you really accomplish is having to report in two states instead of one.
In your case the LLC is registered in Nevada and subject to tax in Nevada, but you operate the LLC from New York, so you should #1 have your LLC registered with the state of NY as a foreign entity doing business in NY and #2 you will have to pay tax to NY state and city based on the profits generated.
The good news is Nevada is a relatively low tax state for business income, but most of your tax dollars are going to go to NY and NYC because that is a relatively high tax jurisdiction.