I am looking for Champions that Jungle incredibly well even if they are not necessarily played often. Specifically looking for champions with fast wave clear and good early game ganks. Basically, I am looking for an underplayed Jungler who is still viable in Season 6. Thanks!
There aren't any. Out of the few junglers that fit the fast wave clear and good early game ganks archtype, there is not a single jungler that is underplayed right now.
It can be argued that Trundle and Skarner (who have fast clears) are underplayed (1% and 1.29% pick rate respectively) but their ganks are situational and are not particularly considered strong early gankeds per League's Standarts.
Xin Zhao, Volibear, Amumu and Udyr are currently strong clearers with strong ganks early on, but they are indeed popular (5-8% pick rate in the jungle) and as such they are out of scope of the answer.
(It's worth mentioning that 5% pick rate is considered popular in the context of Ranked Summoner's Rift - Where each player plays a total of 10% of the involved Champions in the game as as such 5% pick rate is a good indicator of a champion's popularity )