I was granted some NQSO's about 5 years ago while I was a consultant for a company. I became an employee of the company 2 years ago, and am currently still an employee. 6 months ago (while I was an employee) I exercised these options. The difference between the FMV and the exercise price was reported by the company as non-employee compensation on a 1099. Because I was an employee when the gain was realized, should this not have been reported as employee compensation on my W-2?

Nope! Your status at the time the non-qualified stock options were issued to you drives whether the income is reported on your W-2 or on a Form 1099-MISC.

You were a consultant (read independent contractor) when you got the NQSO, so you get the Form 1099-MISC.