I see very little difference between the two:
noun ( pl. -gies)
the body of terms used with a particular technical application in a subject of study, theory, profession, etc. : the terminology of semiotics | specialized terminologies for higher education.
nomenclature |ˈnōmənˌklā ch ər|
the devising or choosing of names for things, esp. in a science or other discipline.
• the body or system of such names in a particular field : the nomenclature of chemical compounds.
• formal the term or terms applied to someone or something : “customers” was preferred to the original nomenclature “passengers.”
Based on these definitions from NOAD, terminology seems a little broader, that is all, while nomenclature seems more systematic and deliberate.