Not that I am going to say anyone that has not been mentioned but I think Armstrong is criminally underrated in this kind of threads during his run. His worst finish on a TT was 7th in 2003 prologue, and his second worst was 3rd, that is simply ridiculous and it is not matched even by Indurain during his peak, he had a big dud in 1995 prologue.
On a seasonal basis, 2009 Contador is quite underrated as well, his TT placements were 1st, 1st, 2nd, 1st, 2nd, 5th, 1st, 2nd, 1st, and his 5th in Dauphine was a result of clearly him holding back himself.