Windows need to be in.
Get the wire into the stud bay first, then finalize once your builder has the windows installed. Preferably, once the window is in, there should be an extension jamb installed, or maybe sheetrock in your area of the country, to fill up the rest of the framing area where the window doesn't sit, vinyl windows generally never are the full stud cavity "deep". Leave about 1-2' in the cavity and another 1-2' pushed through the framing.
The wire needs to be through the framing to it's final location. From that point, either it's an act of faith or communication with the next contractor that is working around the windows or due diligence on your part.