Personally, I never saw Minecraft as a negative for my sons, but I limited their playtime. I see it as one of the better games out there. My sons preferred the creative mode of play in Minecraft. It was also social for them, they could build structures with friends and like Sanne mentioned above, it was very relevant as social currency. They also liked Pokemon and which was great for them socially. I used Youth Digital to introduce them to the coding aspect of Minecraft, http://www.youthdigital.com/mod-design-1.html

Others have already mentioned Lego Mindstorms, which is really great if he is interested in engineering and physics. One of my sons (the engineering inclined one) loved constructing marble runs and building with Keva planks at that age.