I've never had a GGC conure, but I've met several and they would often bob their head in excitement. It's extremely cute. Bobbing can be for several reasons though, hormones, aggression, and excitement. The difficult thing about birds is that their aggressive behavior and excited behavior can be very similar. I assume yours is doing so from excitement though, as you aren't asking about biting too lol.
If you're still unsure try taking a video, videos help so much with behavior questions. It allows us to see all the body languange rather than what is only described.