IDR certification is based on adjusted gross income if you certify your income through tax returns. So if you make $50,000/year but contribute $6,000 to a traditional IRA, your IDR would be based on your adjusted gross income of $44,000.
Regarding the other option, it seems open to interpretation but if ultimately your AGI is going to be lower because of your 403b and 457b contributions, then you might indicate that your income is whatever your gross is each paycheck minus your 403b and 457b contributions, deducted directly from your paycheck (x 26 if you're paid biweekly).