My wife is a citizen of El Salvador and has no SS number

Yes, you probably want to apply for her ITIN.  If she was in the country for at least 6 months, she is a U.S. resident because of the substantial presence test.  You will undoubtedly want to file a joint return, since this is a more advantageous filing status for a married couple.  If she is not eligible to receive a Social Security Number, applying for an ITIN will be the way to include her in the return.  Please see this link with additional information:  ITIN.

To apply for an ITIN:

1. First you must prepare the tax return (Married Filing Joint).  For her "Social Security Number" you will use all nines.  The return will be prepared to be mailed in.  You will pay for the return and print it out.  You will white out any place on the return where your wife's fake social appears and write "ITIN applied" in that place.
2. You will need to prepare Form W-7 (not supported in TurboTax), but can be accessed by clicking on this link:  Form W-7
3. You will provide the supporting identification documents to accompany the W-7 application.  The strongest document is her passport from El Salvador.  Afterwards, she would need a combination of her birth certificate and a photo ID from her country or other governmental source (such as a driver's license or voter ID card).

There are three ways to provide the identification documentation for the IRS:

1. Mailing it in with the return.  (IRS is reliable but you will be without the ID for about 2 1/2 to 3 months).
2. Making an appointment to have it verified at an IRS Taxpayer Service Center (appointment only)
3. Seeing a Certifying Acceptance Agent (CAA) which is generally a private tax professional who has authority from the IRS to verify ITIN identity documentation.

You will then mail in the return to:  

• ITIN Operation
• PO Box 149342
• Austin, TX  78714-9342