You have two problems to solve in your question, both related to modern high-intensity agriculture:
- How to power your fleet of farming equipment with Diesel, and
- How to fertilize the land
Another answer has discussed fertilization by using crop rotation and land management which works, but it doesn't allow the high density that modern agriculture depends on.
This can be solved for your mega city, by spreading out the farms over more land to replace density with quantity. Livestock is a great way to convert inedible plants into edible meats; again, we can't do intensive farming of animals, but we could go back to the Cowboy days of open fields of clover being eaten by livestock.
So the problem really is one of energy post-oil, which we seem to be pretty close to having in abundance. You mention nuclear power; giant hill-scrawling combines can have onboard nuclear generators (or at least radioisotope heat engines). The bug combines could be owned and operated by the city-state, to keep "weapons out of the hands of terrorists" or whatever you want, but we have portable nuclear electricity and steam available today. If anything, feeding a large city without oil would require even BIGGER farms with BIGGER mechanization, so that we can have BIG machines run off nuclear power. The trucks that rotate off the combines could be battery powered; they get topped off at the combine while they're loading and topped off at the silo while unloading.
Oil isn't magical, it's just the easiest form of portable energy we have today. But there's plenty of ways to generate energy without oil; it's just that none are as safe, reliable, or available to the public as oil is today. In a situation where no more oil was available, we would find a way to power the infrastructure to keep us fed; especially if we're only worried about one city-state.
Science and nodules. One other thing. Clover is so useful because it's got symbiotic bacteria that fix nitrogen and the like in the soil. Cows eat the clover to produce manure which then fertilizes the fields. I know you said that recovering waste from the city was a no-starter... but why? If we recovered the human waste from the city and used nuclear power to process it, it could easily fertilize fields. And biotech firms in this future would probably crack the fixing problem in giant tanks of bacteria; we're not worried about it today because fertilizer is still relatively cheap.