Well, much will depend, actually, on where your intake fans are (if any) and where your exhaust fans are located. By the way it sounds, the majority of your case is housed in a very tight enviroment (sides, top, bottom and rear) and what little space is around those sections is probably encased in hot exhaust air from your rig. Even if you have cool air coming in the front, what you are lacking is a secondary source of cool air (preferrably the side). In a cubby hole, even if you have side intake fans, what air will they be able to draw from? Probably the air that is flowing insied the cubby hole that is, largely, heated air created from the exhaust fans. (In this, I am just assuming that only the front of the computer is exposed).
If possible, in that cubby hole, could you cut away holes (for the exhaust and intake fans) so that they have access to cooler enviroment air? Ideally, if you could have air drawn in from the front and sides, and exhausted from the rear and top, you would have a much more efficient airflow stream and would see system temp drops more inclined to what you had hoped for.