You could get the produce packing station from SimWardrobe.com. Twelve of each fruit/veggie fit in a single crate from that station. And selling them from an OFB store is more profitable in crates (too profitable, actually, but I have a mod for that
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You can also just store quantities of the produce in the fridge for use. You won't be able to get it out again though. It's used for cooking meals.
Or you could store it in the juicer. There is even a mod (by Monique, if I remember well) to increase the Juicer's capacity.
And yes, PlatinumPlumbob is right: your farm(s) may be too large. Sometimes, I have a sim run a greenhouse with 48 plots (that's three squares of 4x4), and even with my lower prices mod, such a sim rakes in the dough hand over fist. So even that is too big.