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You can remotely open the windows and sun-roof by holding down the 'open-lock' button on the key fob for about 3-5 seconds, but there is no specific feature to close (or open) only the sun-roof remotely.
According to the owner's manual (2007 ES 350, pg 405), there are a multitude of functions that can be customized involving the key fob. The sunroof activation is one of these functions. However, these functions can only be customized by the dealer service department. If your sunroof does not function with the key fob, but your windows do, it is likely that this function was turned off. I would call the dealership and ask what needs to be done to change this.