For educational purposes I need to compare the performance of WebGL with OpenGL. I have two equivalent programs written in WebGL and OpenGL, now I need to take the frame rat
You actually do not want to use framerate to compare these things because as you just mentioned you are artificially capped to 60 FPS due to VSYNC.
The number of frames presented will be capped by the swap buffer operation when VSYNC is employed and you want to factor that mess out of your performance measurement. What you should do is start a timer at the beginning of your frame, then at the end of the frame (just prior to your buffer swap) issue glFinish (...) and end the timer. Compare the number of milliseconds to draw (or whatever resolution your timer measures) instead of the number of frames drawn.