If her Social Security application is currently pending, I'd file an extension and wait for the Social Security number so that you have an easier filing situation going forward.
However, if that application hasn't yet been started or she's not eligible for a Social Security number, then you can apply for the ITIN with the return attached. The ITIN Operations department will forward your tax return after they issue her ITIN with the date stamp of the date of receipt in their office If you apply for an ITIN, I recommend filing an extension anyway just to cover your bases.