UBM TechInsights has done a teardown of the Nintendo 3DS and marks the total cost of the system's hardware at $101. That's $15 more than the DSi was reportedly made for, though the 3DS also includes a 3D screen and a gyroscope, along with other enhancements.
Retailers are selling the 3DS for $250, but that's not all markup -- there are marketing, research and other charges associated with a console release, and everyone in the supply chain has to take their own cuts, of course. Still, Nintendo is likely making a profit on every unit sold, which is exactly as expected (and what it did with the Wii). Even before you start talking about games and licensing, Nintendo is making sure there's some money rolling back its way from day one.