Controls on top, Con: At the angle you are viewing the monitor, the joystick (and your hand) would probably block some of the view. It could be fixed by giving more space between the monitor and controls, but then you would have a more difficult time seeing everything.
I don't know what the table looks like, but could you build the controls the same distance, but lower? For example, could you make a control panel hanging down from the underside of the tabletop at the edge?
If you can't mount them in a way that you are completely satisfied, then I would say don't bother. The time and effort wouldn't be worth the result.