"No son meses, sino años."
despite it being plural in spanish, it makes no sense to do that in english. The 'it is' refers to a timeframe (which is singular). It's unlikely to use this phrase in present tense, but sounds fine in future tense. eg "it will be years, not months, before the job is finished".
I can't think of any context in which "they are not months, but years" would be meaningful.