In 1940, when the phrase was first used in Radio, airplanes were still uncommon, especially in the city. It's been explained that if it were a plane, the lack of engine noise would be peculiar. Also, the actual size was actually to small for a plane of that era, prompting them to believe it a really large bird. Of course, the cheesy line also set about the excitement boys and girls would experience in the next 15 minutes of the tadio program.
And, yes, the phrase did appear in the comics years later as a homage to its radio heritage.
The phrase is so iconic, today, that it's found its way in other comics for comedy relief. It's also on of the earliest reaction gags young children learn as they point up and day, "Look! Up in the sky! It's a bird! It's a plane!" Pause, wince, wipe eye and say disgustedly, "It's a bird".
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