If your wife as a non-resident of NY never physically worked within New York State - not even for a single day, then her income from her remote work is not subject to NY income tax. NY does not tax the income of non-residents who never physically work inside NY. It does, however tax non-residents on income earned from work actually performed within NY.
Since she is a resident of CT, all her income regardless of source is taxable by CT.
What forms is NY asking you to complete?
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
