1) The relief u/s 89 is given when the arrears of salary are received across the years. In your case, it appears that the retention bonus was given in the year, which was declared after you left the organisation but applicable for that year. Hence, the income will be considered as the income for the FY 2016-17.
2) As you are probably resident of US, you need to declare your global income, i.e, the income earned in India. You will get credit for the taxes paid in India under DTAA.