I would think it is more likely the shock. I had a noisy one on my last bike and shortly after it started leaking. Was replaced under warranty for the leak but it fixed the squeak also. There are several pivot points in the linkage at the shock and these are easy to access and lube so I would start with them.
Having said that I just finished cleaning and repacking my swing arm bearings. Just like my last bike there is very little grease in them from the factory. There are just two - one on each side. I did this just in the interest performing the routine maintenance but especially since I was aware how Yamaha skimps on the grease. Factory recommended lube interval is 24,000 km so I can see the dealer wanting to charge you for the repair due to lack of maintenance assuming you hadn't performed this.
On the subject of scheduled maintenance and bearings, two weeks ago I pulled the triple tree off to clean and repack the steering head bearings. Just like the swing arm bearings they have very little grease from the factory and also are due at the same time as the swing arm.