I am not sure as to what the question is. If you have been married in another state, you can certainly get divorced in New York as long as the residency requirements are met. If you are not legally married, then there would be no need for a divorce. Much will depend on exactly what type of civil union there was, and what rights attach to it.
There would be no need under current laws to file for a legal separation first.
I have been an attorney in New York for over 20 years. Feel free to view my website at Brooklynlaw.net or contact me either by phone at 718-208-6094 or via email at firstname.lastname@example.org. This answer is only for informational purposes and is not meant as legal advice.
It may be that even if you are not married, you and your partner may need to enter into an agerement that separates your property. This can be done by any qualified attorney who practices matrimonial law.
Please be advised that this answer shall not constitute legal advice, or create an attorney-client relationship.
As always, do not construe posts as legal advice but as "attorney advertising" and you should always consult with a lawyer on any legal matter.
I would also suggest you retain counsel in the state that you had your civil union.
A weekly guide with tips and legal advice for each stage of the process.