Both are acceptable but mean slightly different things. "To make a space" implies that a specific open area is being made for a specific purpose or object in a particular location. "To make space" is more vague and relaxed and denotes the creation of more available space in general. In some cases one is more appropriate than the other, and in other cases both would work. As a native speaker my ear has a preference for "to make space" so I'd prefer that form if there is overlap.