If Stalin dies or is replaced in 1941 there is no way that Zhukov would replace him. Zhukov didn't have the political powerbase until 1945 at the very earliest, in 1941 he was just another Soviet commander in terms of political power. IOTL, Zhukov was easily purged from power postwar when he was seen as getting too big for his boots. Even when Zhukov had real clout he was removed by his rivals. The Soviet Communsit Party was always paranoid about the Army taking over as they knew many of them would end up getting shot, and no Soviet commander was ever allowed to lead the USSR. All Soviet leaders with military experience, e.g. Kruschev, were political commissars, not field commanders. The circumstances of 1941 will not change that central rule of Soviet politics.
Beria's fate IOTL indicates that he had little (or no) support amongst the Party or the Army as well, as soon as they could they got rid of him. It's possible that Beria might grab power in an alternate timeline but he would have to have taken it by force, neither the Party nor the Army would grant it to him. This may have led to considerable confusion in the USSR as some nasty purges would have been required to thin the ranks of his many powerful enemies.
I'm not sure who it would be, but any replacement for Stalin would most probably have come from within the Party, not from the Army or the NKVD.