It depends, generally couples are better off filing a joint return. There are some tax credits that you may not be eligible for if you file separately and your standard deduction is $25,550 when filing joint instead of $12,550 when filing separate. If you do not have itemized expenses greater than $25,550, then filing jointly will lower your taxable income which will lower your tax liability since her income is only $1,000. So, you may be better off tax wise to file jointly this year.
If you choose to file separately, you will still need to print and mail your return as a separate return still requires you to enter your spouses Name and TIN. Since she does not have one, you would need to include her name along with a brief explanation of why you do not have a TIN for her.
Note, filing a joint return is different than claiming someone as a dependent. Spouses cannot be claimed as dependents. They are "Co-owners" of the tax return.
If you are filing jointly, you will need to print and mail your return along with the W-7 and any other required documents to
IRS
ITIN Operation
P.O. Box 149342
Austin, TX 78714-9342
Whether you file jointly or separately, you will need to print and mail for this year.
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