I would advise against using a window -- it is hard enough to get proper skylights not to leak, a window without extensive flashing is likely to be a lost cause.
The simplest thing, by far, is to use plastic roofing and make one of the panels translucent or transparent. Beware excessive heat gain, especially in a small-volume coop, though; at the very least, best to put it on a north-sloping roof and make sure the coop has LOTS of ventilation that can potentially be opened up.
If you really have your heart set on a shingled roof, best to use a skylight with all its appropriate flashing... but it may still leak a bit, especially if you are using a secondhand one (often they're secondhand *because of* leaks, some of whcih are installation issues but others are structural to the skylight itself).
JMHO, good luck, have fun,
Pat