There are two kinds of rarity in CryptoKitties, immediate rarity and long-term rarity.
To find out what traits are rare RIGHT NOW, the best tools to use are CryptoKittyDex or the KittyExtension. They tell you the current rarity of traits. You can also check the news section of my sidebar to see what traits have just been released. The newest traits are the rarest ones in the immediate time frame.
If you want to know what traits will hold their rarity for a longer period of time, check out the Trait Chart. The traits near the bottom are mutations. The darker the blue, the more mutations it requires to breed into that trait. Those traits are usually more rare in the long-term, especially in low-generation cats.
(And if you want to know what traits will be rare in a REALLY long time, look at the boring basic traits that everyone is trying to breed out of their cats. If everyone is trying to mutate out of those traits, it’s possible that those original basic traits will slowly become rare over time. [Excepting totesbasic, which currently has three genes that map to it.])
Want to know more about rarity? Check out this post on which cats are rare and desirable.