This probably wont answer your question but it might help. First of all input lag is a misnomer, it's not latency on input that's the problem, Vsync is a latency on processing/output. 2nd of all it's really not easy to measure in software alone, measuring true latecy between input and output can only really be done with cameras watching the monitor and input devices.
One thing to keep in mind is that with windows from Vista onwards the desktop has vsync enabled and some games in window mode may conform to a type of vsync because of this, I'm not 100% sure how this works but I think for your particular problem/question that's worth investigating. Even if the 3d rendering of the game doesn't have vsync, if the desktop as a whole has it, and it's a windows inside of the desktop you may get unexpected results.
Hopefully someone can elaborate on this.