The FAQ doesn't have a specific entry about comment rankings, but I'd guess it's based off a similar system as the Stories rankings: "How are stories ranked?

The FAQ doesn't have a specific entry about comment rankings, but I'd guess it's based off a similar system as the Stories rankings: "How are stories ranked? The basic algorithm divides points by a power of the time since a story was submitted. Comments in threads are ranked the same way. Other factors affecting rank include user flags, anti-abuse software, software which demotes overheated discussions, account or site weighting, and moderator action."