Theres no way to know that. Nintendo has never released numbers that didnt include everything, including the VERY successful GBA. But common sense would say that at the price the cube is going for vs manufacturing costs and R&D its a cash drain. How much of a drain is debatable but there is no way it can already be in the black.

Planetgamecube reported that the production costs of the GC are $100, but like you said that doesn't include things like R&D.

There were some reports that they were making a profit before the price drop though, but I don't know how reliable they were.

I don't know anything about the PS2's costs.

I'd say it's pretty safe to say all systems are losing some money right now, with the X-box losing more than the rest (costs were estimated a while back at $325 per console factor in 2 free games now and paying sega to agree to it).

Nintendo has always been efficient and cutting production costs pretty quick and making profits on consoles in the last half the systems life span (or so I've read) so they probably do a decent job of earning back some of their losses. But with no solid data, there's no way to know for sure.