My father is an Indian, acquired his green card due to the death of our mother in 2008, and is trying to wind up affairs in India... he wants to transfer his money from an Indian account to a US account. Does he need to declare his Indian income to the IRS, if yes, then above what level?
If he makes a wire transfer from his account in India to his account in the US in excess of $100K does he owe taxes to the Indian govt and the IRS, or just the difference? Say, his tax owed to the Indian govt were $12,000 and what he owed in the US were $15,000, would he then owe $12,000 and $3,000 respectively?

Transfers are not income. They will be reported to the IRS, but are not income. When he files taxes in the US, he will be asked about foreign accounts. Note in return that assets were liquidated and/or transferred would probably be fine for the same reasons you said. Any transaction over $10k whether it be buying a house or car is reported to the IRS.
Not claimed on income.

I'm a US citizen. If I had an account in China. I would report the interest income on my US tax return.

Now, wire transfer fees could be amount based. There might also also be currency conversion fees. Shop around. There may also be restrictions as to home much can be transferred.

Thanks a lot!