+1 on trans oil. Water will fry those bearings quick. Also, I've heard on this forum that a leaky odometer reset button can leak water through the gauge, down the speedo cable, and into the trans. Something to worry about

The driveshaft boot can indeed let water in the swingarm, and it's the most likely suspect. Not a whole lot of oil in there, so it doesn't take much water to make it look pretty bad. The only other ways water could get in is past the gasket between the swingarm and final drive (not very likely) or from a leaking transmission output seal (from a transmission with contaminated oil in it).
If your trans oil level is good and the oil clean, that rules out leaking contaminated oil from the transmission.
My final drive tends to overfill a bit from the swingarm and leave the swingarm low, but the swingarm will never run dry. Some people don't put the full spec'd amount of oil in.