Just make her sit in the middle seat (which is safer anyway). A three-year-old's arms aren't long enough to reach the handle from the middle seat. She can only unwind a window when she is sitting in the seat next to it.
Mechanical windows require mechanical locks. Electric windows just need an off switch.
You have few choices.
1. Remove the crank so no one can open the windows.
2. Epoxy the windows so they can not be cranked open.
3. Move the crank handles so when the window is closed the handle is down. Then tie it with a rope to the bottom of the door.
4. Put a hole in the handle and door and stick in a long screw so the handle can not be turned.
5. Put your kids in car seats so they can not reach the handles.
6. Teach your kids not to open the windows.
7. Buy a new car with electric windows then turn them off.
I don't think there is a way to lock the windows, but you could remove the handles. Here are a couple of websites that tell you how to do it:
http://toolmonger.com/2009/03/03/how-to-...
http://wiki.answers.com/Q/How_do_you_rem...
If she is controlling you at 3 just wait until she is 15. Time to take control.
Kid has you trained. I trained my kids. My kids learned quickly that I am willing to spank, no warning, no constant saying "no."
remove the crank habdle
not that i know of iv never heard of locks for manual windows