I think you are in a grey area that can go either way. My view is that you have a closer connection to the New York client that the California company so you would pay NY tax. But it can be argued either way.
You could discuss you situation in detail with a New York accountant or tax attorney, file and pay tax to New York and then file an amended return asking for it all back. An amendment is like an appeal, so there is no penalty if you were fully paid up and your amendment is denied. So you could simply not file in NY and see what happens.
New York Source Income—Sole Proprietorships and Partnerships
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