There are all sorts of factors that make individual mission pay a headache to simulate properly, but I can give rough annual figures for Clanless Chunin & Genin based on their economic contribution to the Land of Fire:
A Clanless Chunin generates R300,000 of economic value per year. If the average clanless ninja is on a mission for 200 days out of the year, raw market rates for average Chunin mission pay should be R300000/200 = R1500 per ninja per day.
A clanless Genin generates R125,000 of economic value per year, so 125000/200 = R625 per ninja per day. A genin without a clan might see R20000 in disposable income per year.
Of course, this does not account for missions assigned by the Kage out of military need, which may be the majority of the missions available and could drive up the price considerably. If we say that military missions constitute the majority of missions taken, we can probably handwave a rough doubling of overall mission prices, so R1250 / day and R3000 / day for clanless Genin and Chunin, respectively.* This is all pre-tax income of course.
Clan ninja are more effective on average so can take more difficult missions, say R2000 / day and R5000 / day respectively.
As for jounin, power levels vary wildly so average numbers would be less representative, but assuming five times the Chunin rate then it would be R15,000 - R25,000 per ninja day. S-rank probably 3-5x above that.
The Kage has a considerable budget surplus from unclaimed Clan Benefits**, and can also utilize fractional reserve banking + war bonds, so can easily afford to pay aggressive rates for military missions. They're getting much of it back in taxes anyway.
*In reality, there are two tiers of missions: the relatively safe "create economic value" missions given by civilians, usually involving chakra beasts or security duty, and the relatively dangerous "military necessity" missions assigned by the Kage. The former would pay R625 / genin day and R1500 / chunin day, the latter paying triple that but requiring more intensive use of resources (seals, healing time).
**Founding Clans need to average R16250 of benefits per ninja per mission day, which is unrealistic for anything but a clan composed solely of jounin. In reality, most Founding Clans probably work their asses off just to hit 50-75% of conditional benefits. Conversely, non-Founding clans only need to hit R2980 of benefits per ninja per mission day, very attainable but much less money overall.