The Great Nations of Europe

What examples from the song are ironic?
he met some friendly Indians whom the Church told him were gay,
soooooooooooooo
he had them torn apart by dogs on religious grounds they say
the great nations of Europe were quite holy in their way.

Columbus sailed for India found Salvador instead.
He shook hands with some Indians and soon they all were dead.They got tb and typhoid and athletes foot, diphtheria and the flu

'scuse me great nations comin through

How can you tell?  
It's ironic because he says that Balboa met some friendly Indians, but then he kills them because the Church assumes they are gay. Also, it says the great nations of Europe were quite holy in their way, he is actually referring to the opposite. They killed innocent people with the excuse they were gay when first, that shouldn't be a reason to kill and second, they were not certain of that making them everything but holy. 
The second sentence is also ironic because when he says he shook hands with some indians, we may think that it was as a good start, like they were making friends and were going to be treated correctly. However, it is actually because they shook hands that they got all the diseases and they soon were all dead.

What examples are not ironic?  
They'd conquered what was behind them and now they wanted more,
so they looked to the mighty ocean and took to the Western sea -
the great nations of Europe in the 16th century.

Now they're gone, they're gone, they're really gone.
You never seen anyone so gone.
There's pictures in a museum, some lines written in a bookbut you won't find a live one, no matter where you look.

How can you tell?
This example is not ironic because it is true. The European nations had already conquered Africa so when they discovered America they saw it as an opportunity to get more colonies,  show their superiority to other colonizing nations, and to get raw materials. the author is saying exactly what he wants the reader to understand.
When he says they're gone he is refering to the indians who were exterminated and their culture was completley lost. He says that there are pictures in meuseums and limes written in a book which is true, the culture was entirely lost and the only place we can find somethings about them is in books and meuseums, there is no way to see them physically alive because they are gone.