Common "house fly" maggots do drown (all maggots do, unless they happen to be an aquatic species, which would be extremely unusual to come across, but some larval insect stages, such as dragonfly nymphs, do live underwater). Their mouthparts and breathing apparatus are not adapted to underwater living, and their metabolism is much to high to support an "air bubble" ecology like some diving beetles).

Maggots are carniverous, and will not eat vegetable matter in a clogged drain. They do have a certain amount of chitin (what makes insects "hard", or crunch when you step on them for example) in their larval shells however. And if they pupate (start moving to the final fly stage), even more chitin will be produced. This stuff is going to be very difficult to get rid of, it will not break down in the same way, or react in the same way to drain cleaners.

If you really wanted to do this, in general from egg to fly takes 12-14 days, so the major "eating" stage for your purposes will probably be around 9 days. If you don't mind being without a drain for two weeks, never run water in it, take your chances with vegetable matter not being consumed, and are willing to have particularly filthy flies emerging from your drain at the end of the ordeal, I hope this gives you some insight. But for all these reasons, I would strongly, strongly recommend calling a plumber or cleaning the pipe yourself. You are concerned about a green method of cleaning, there are totally mechanical methods for opening/cleaning a pipe that involve no chemicals. I've used some of them, you can find all the information and tools at Home Depot.
Source(s):
http://www.ext.vt.edu/departments/entomology/factsheets/housemag.html
Personal experience (with cleaning pipes, not using maggots)

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