There is no best. The best approach will vary from game to game. This is because not all vsync implementations are the same and not all game engines or games behave in the same manner.
In keeping with this, the answer to your specific question is; it depends. Yes, if you're using vsync with double buffering. No, if you're using another implementation such as adaptive vsync (which can be forced as a nvidia driver option, but rarely implemented by developers in game), or vsync with a render ahead queue.
I suggest you read this on triple buffering from Anandtech. http://www.anandtech.com/show/2794
It's useful background and importantly explains that DirectX does not feature true triple buffering and in fact utilises an optional render ahead queue. If your game is 32-bit, you can use D3DOverrider to force on this queue, which will prevent the problem you describe.
Anyway, you will need to experiment. Sometimes the in-game vsync is best, sometimes it's trash. You can use the utilities you mention to cap the framerate and GPU drivers to enable vsync. There's also nvidia inspector (for nvidia GPUs), which can be customised to add in your own arbitrary cap value. I think RadeonPro is also useful, although I've no experience with it personally.
