I'v heard various opinions about which Amoraim can argue with Tannaim, ranging from any, to only Rav (Rabbi Abba). Which Amoras can argue with Tannas?
Rav Yochanan and Rav aren't entirely amoraim; both had semichah before the mishnah was closed. I bet there are a number of first generation amoraim in the same boat.
Shmuel is more complicated, since he never got semichah. However, the Rosh compares Berakhos 23b, where we rule like Shemu'el even though he contradicts a beraisa, and 24a where we wouldn't. The Rosh says that an amora can dispute a beraisa because a beraisa isn't a reliable enough record of the tanna to be sure that's really what the tanna said.
So he would seem to rule that an amora cannot disagree with a tanna, so if we have the tanna's in a mishnah or tosefta (more reliable sources), the amora cannot disagree.
At http://www.aishdas.org/avodah/vol06/v06n098.shtml#03 Eli Turkel summarizes an article by R' Zalman Koren which lists numerous opinions. There is another survey by R' Mechy Frankel here http://www.aishdas.org/avodah/vol02/v02n003.shtml#13.