I think you have to take into equation that Sagan rides a lot more races which suit his characteristics than EBH does. Liquigas is very good at sending Sagan to races with many reduced bunch sprints which he excels at, whilst Sky seems to prefer to send EBH to races like Qatar, Bayern etc. Also they have more or less never raced vs each other. The only occasions in the last 2 years they have been in the same race is Canada last year (EBH 2nd in Quebec, Sagan 19th whilst in Montreal they both were in the 6 man chase group before EBH fell) and worlds this year (EBH 8th, Sagan 12th).
I'd say EBH is currently the better rider as he has a slightly stronger sprint, about equal climbing, but much stronger time trial. However, Sagan is younger so might be slightly more talented. That being said, at 21 EBH had won G-W and a stage at the Giro, both bigger victories than anything Sagan has won as of yet.