Now, this is a really tough one. On the face of it Nibali is the least suspicious, and after his Giro win and his riding for Astana and having been connected to Ferrari that's pretty surreal.
However, it was a tough competition in the way of crazy suspiciousness this year. In many years Richie Porte riding such a fast Col d'Èze TT (looking like smashing the record of the guy he was not even the #1 domestique for the previous year) that Séan Kelly, who we may remember knows a thing or two about cycling - and doping - stopped to ask if there was a timing error because the time was so preposterous, would have easily been the most suspicious performance of the year. But this year, no.
This year is almost impossible to choose, since Froome's general level has been red flags waving, klaxons blaring, screaming obscenities dope-suspicion all year, but with his being at least in a cyclist's peak years on his side he comes up against stiff competition from Papy Horner, who for all the crap we give Froome about his early career, had only won a couple of domestic competitions by the time he was Froome's age, failed miserably when riding for FDJ (although they were shady at the time, they are now considered one of the cleaner teams in the bunch) and returned to Europe in his mid-30s with Saunier Duval (considered a very shady team), and has continued to improve in level into his 40s in the most preposterous of manners. I mean, from scraping 10th in the Tour after gaining several minutes in breakaways at 38 to winning the Vuelta with multiple mountaintops and by being the strongest climber at 41, it's just stupid.
Can it unseat Chris Froome? It's a really agonizingly tough pick, because pretty much everything about Chris Froome is suspicious, while people genuinely want to believe in him. Even those that support Horner don't believe in him and just want his ridiculousness to show up how hollow the calls of cycling having changed truly ring. I think over the course of the whole season, Froome, but for a specific race that was most suspicious, Horner would take it.
I'd also add in the category for suspicious non-performances of 2013, i.e. how the chronically poor seasons endured by Bradley Wiggins and Alberto Contador make their 2012s look. At least Cobo has the medical explanation.