Worked in MA, earned 50,000. Also self-employed, 6,000 from NY (before deductions). NY tax return includes ALL income, says I need to pay taxes on the entire $56,000?

I worked in MA and earned 50,000.  I also had a separate business and $6000 was paid from a NY-based company.   I'm not sure I need to file a NY state return for the $6000 but when I did it through TurboTax, it included the entire $56000 on the taxes and said I owed over $300. Does this make sense?  The only income I got from NY was $6000, which would be even less after business expenses.  

Any suggestions?