I agree that both courses are important. It really depends on what you want to do with computers. If you are hoping to sell computers or work for a retail company, the commerce class might be more appropriate. If you are hoping to work in other areas, the science courses are probably better. Many computer programmers do not deal with the commerce side of the business. They often do not even interact with the customers or manage the business at all. Physics can help you understand the type of linear thinking and problem solving needed for computer repair and programming. Chemistry can help you learn to complete complex conversion and mathematical computations similar to those used in some program codes. Unless you are planning on owning your own business or working in retail, I would say that the science courses are going to be more beneficial than the commerce class.
Sciences that are very closely related to computer science are mathematics, physics, logic and electrical engineering. Of course commerce can be useful in any field of work but if you want to know more about computer programming, microchip design, computer networks, Internet etc. I believe you should take some of the courses I mentioned above. Not only because you can learn how to use different mathematical operations in your algorithms or learn how transistors work, but also because those sciences require similar "way of thinking" as computer science. So in a way you would also learn how to think as a programmer before learning anything about computer programming.
I think it depends on the science class. If you are involved in computer science, they may require other science classes. A commerce class might be useful if you are seeking to market a computers-related product, such as an app or game.