With vsync enabled where does the wait happen in OpenGL?
It's a bit complicated because the actual wait for vsync does not happen on the CPU, it happens on the GPU. The GPU wait then creates back-pressure that propagates back to the queue of submitted command lists on the CPU, through the GL driver, and eventually to your app. The exact behavior will depend on the details of how the GPU vendor chose to implement their GL driver, and also probably depends on the behavior of the windowing system as it controls frame presentation. Unfortunately there are no real guarantees about this in GL as far as I'm aware, it's really up to the vendors.

In this case, it seems likely that you're seeing the wait become visible to your app at the first GL command that causes the driver to try to begin recording into a new command list (which may entail waiting for a previous command list to finish executing on the GPU, so that the driver can reuse it for the new frame). Clears, draw calls, dispatches, buffer mapping or copying, etc would probably qualify, while (for example) state-setting calls or memory allocation calls might not issue any actual commands to the GPU.