The reason EA is not Indie is because they are a publisher. Other, smaller companies make games for them. For example, DICE made Battlefield 1942, but EA funded/published it, because EA has the money and name to get it out there.
Mojang is indie because they made the game, AND they published the game. DICE, had it funded and published Battlefield 1942 themselves, they would have been the big Indie publisher on the block at the time.
Now, if Mojang starts spending their money to fund other developers, and publishes a game for them, then they would be on the road to becoming a major publisher.