alphagc,
It is the process how obtained your Green Card (Employment based or Marriage based) that defines the process of Naturalization. Your marriage to a US Citizen is a life changing event for sure but it did not affect your Permanent Resident Status.
Since GC petition was approved based on Employment requirements, hence 5 year eligibility requirements will apply for you. I know, 3 years would have been ideal, but that is not how USCIS will look at it.