That would be correct. However, to file married-separate in New York, you will have to complete a separate federal tax return for your spouse so she can file as married-separate on the federal return in order to get the state return populated properly.
You may want to use the desktop version of TurboTax where you can complete several federal returns without having to set up new accounts and pay additional fees for the TurboTax products.
Also, if you file married-joint for New York, your income in Texas will be factored out to some extent, so it may be easier to just do it that way and it shouldn't cost you much in additional tax.
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