When Tony is in the coma Silvio says to his wife that "the old man" before he went away wanted him to be the boss. Just about everyone has it right i believe, Tony was the street boss and basically over looked all operations with junior acting as boss but there are two different periods in his reign. Before the failed attempt on tonys life and for a couple of episodes after junior's thoughts were actually listened to and acted upon by the rest of the capos. But after they kill off juniors guys, and leave him with bobby and a bunch of old guys to take care of his operations, he is only boss to take the heat. Junior also works in the capacity of boss in many different situations such as meetings with NY over johnny and Ralph's troubles and when carmine dies leaving a power vacuum. Tony is the boss de facto but is modest enough not to need the title, he knows he is the boss just like everyone else does.