It is Colchester, and promotion into the Football League from the conference was only initiated in 1987.
Other teams joined the league, for sure, but then the question would be who is the highest placed team other than the original founding teams, and the answer would immediately be Chelsea.
If you include the election (not promotion) process which operated from 1962 or thereabouts, the answer (I think) would be Wigan.
PS Willem, no, that's not what I meant. I meant all of the premier league would be above the Coca-Cola Championship (the second tier of English football), who all in turn would be above the League One teams (the third tier).