If you are using a joint federal return to create a NJ return then your spouse's income will be included. The best way to handle this situation is using the link @MayaD posted and a TurboTax desktop product where you can create several returns in the same product. Here is that helpful link again.
You will create and file a joint federal return. Then create a "Mock" federal return for you with only your income/deductions. From that "Mock" separate return you can create your separate NJ resident return and non-resident NY return. Work the non-resident NY return first so that TurboTax can use the income taxed in NY and the NY tax liability to help you claim a credit on your NJ resident return for taxes paid to another state. That mitigates the only double taxation. You will need to print/mail your NJ and NY returns since you are not actually filing the corresponding separate Federal return.
You will do the same for your spouse. Create a "Mock" separate federal return with only her income/deductions. From that "Mock" federal return, you can generate a separate CA resident return. The CA return will need to be printed/mailed.
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