You measure the differential output noise by specifying the two output nodes to the noise analysis (if you specify one as ground, you would be measuring the single ended noise, not the differential noise).
To measure the input referred noise, you must also specify the input source.
An alternative approach, that is more powerful, is described in a paper called "A test bench for differential circuits" that you can find at
http://www.designers-guide.com/Analysis.
- MM -