Get window position and size in python with Xlib
You are probably using reparenting window manager, and because of this id window has zero x and y. Check coordinates of parent window (which is window manager frame)
Liss posted the following solution as a comment:
from ewmh import EWMH
ewmh = EWMH()
def frame(client):
frame = client
while frame.query_tree().parent != ewmh.root:
frame = frame.query_tree().parent
return frame
for client in ewmh.getClientList():
print frame(client).get_geometry()
I'm copying it here because answers should contain the actual answer, and to prevent link rot.