I whipped up a quick reflex tester ROM which I hope to clean up another time. When run, it makes the screen white and waits for your to press A to seed the random number generator. It clicks and delays for 2-6 seconds, then clicks and makes the screen white. At this point you should press A as quickly as you can. It prints the number of milliseconds between the screen changing and you pressing A, then waits for you to press A to start another trial.
Take several times and average them for better accuracy, since the figure varies by many tens of milliseconds. On an emulator that only reads input once per frame, measurements will always vary by a multiple of 16.6666.
I took measurements for several setups involving my NES and an emulator on my PC with a CRT refreshing at 76 Hz. For each setup, I took 12 times and found the average. For audio, I used headphones.
189 Video, NES on TV
194 Video, NES on video capture
227 Video, emulator using custom serial joypad
236 Video, emulator using keyboard
254 Video, emulator using keyboard, vsync enabled
231 Video, emulator using custom serial joypad, vsync enabled
191 Audio, NES RCA out
254 Audio, emulator using custom serial joypad
Take your own measurements and post them with a description of what you timed. reflex_timer.nes