Junior, I believe, was the actual boss until the point, in which, he shot Tony at the beginning of Season 6. Of course, we all know that Tony put Junior in charge to be the lightning rod for the FBI and that Tony had effectively been in control since the hits on Philly Parisi, Mikey Palmice and Chucky Signore took place and Junior was arrested.

Was it ever mentioned that DiMeo died? I always thought that a boss stayed the boss until death or abdication. Unless, he abdicated from prison wouldn't the pecking order be like this throughout the entire series:

DiMeo as Boss (albeit he has no power whatsoever, but still holds the title)
Jackie/Junior/Tony as acting/street boss (but not necessarily answerable to DiMeo in prison)

I guess to not confuse the average viewer they may have just left DiMeo out of things after awhile.