Basically you need to prepare 3 returns. You will want to buy turbotax Deluxe on CD or as a download, because if you prepare these returns online, you will need three accounts and pay 3 separate fees. The other experts should have posted links to specific instructions, but in general this is what you will do.
1. Prepare a federal return as married filing jointly. You can e-file this return. Do not prepare a state return.
2. Prepare a federal return for your spouse as married filing separately (MFS). Include the CA state return. Ignore the federal return and print and mail the state return (it can;t be e-filed in this situation.)
3. Prepare a federal return for yourself as married filing separately (MFS). Include the NJ resident return and the NY non-resident return. Allocate your income carefully; income from working in NY is NY income, but other income (maybe interest and dividends, investments, passive real estate income, etc) will be NJ income only. NJ should give you a credit for taxes paid to NY. Ignore the federal return and print and mail the NJ and NY returns. You can't e-file your state returns in this situation.
