Hens are NOT quiet, as anyone who has spent time around them can attest. I don't know who started the rumor that they are quiet. Maybe with a rooster, they aren't as noisy; I've read this, somewhere. But hens seems to "fill in" the missing rooster's noises with sqwaucking that seems louder and longer than any rooster's crowing I've ever heard.
Anyway, in an urban setting, it seems early morning is the worst time for the extra noise. You can try the following to shut them up:
1. Insulate the coop (according to some people this works by muffling the noise) & don't let them out til 8am.
2. Give them earlier & more free-range time (my hens are very quiet when free in the yard, compared to the run)
3. Put interesting treats in the run, for early morning entertainment (like a flock block, or seeds sprinkled, fruit cutups after they've gone to the roost)
You can mask the noise somewhat by creating a "bird-friendly" yard. Put up feeders, plant native shrubs, bird baths, etc. This will bring in all sorts of wild birds which make lots of noise early morning. It can help to mask the noise your birds make, especially if you can attract crows. Now, that's some serious CAW-CAW-CAWing to compete with your hens' noise.
You can give your neighbors fresh backyard eggs. And if they don't like eggs, give them some fabulous chicken litter for their gardens. This helps mask the unpleasantness they could feel about your birds. It could help them feel more connected with them.
I don't think the flies are what is causing the noise. You can dry out their litter with food grade DE, but it is usually boredom and the fact they want OUT, or they want new treats or food, and, if you interact & talk with them a lot, they are accustomed to interacting and talking to you.
Last, if you have a chance gently remind your neighbors about how they already live with a lot of obnoxious urban noises:
1. A screaming chainsaw and its horrid gasoline fumes, forcing you inside on a really rare sunny day
2. Stereos and boomboxes played at high volume from decks and patios, for the entire neighborhood to hear
3. Howling or barking dogs
4. Weed-whackers, leaf-blowers, lawn-mowers
5. Pressure-washers, used on houses, decks, sidewalks, driveways
5. Construction noise, like table saws etc.
6. Air compressors, used in nailing construction
7. Air conditioners
9. Neighbor parties, held during the evening and night hours.
10. Drunk neighbors, talking loud on cell phones or fighting
11. Screaming children
12. All the other urban noise blasts, like sirens, cars gunning their engines, blasting horns, fireworks, and other explosions, etc.