What camera would be better for macros/ close ups?

Either canon 1000d or nikon d3000

Neither, both

Both cameras are capable of shooting macros if you have a macro lens.

Yes, as fhotoace stated, macro will depend on the lens. If you get the kit lens (18-55) or any other lens actually, you can have a reverse mount and flip the lens around to get very good macro photos. The thing is, you need very bright light, only works in manual focus, and may scratch/dust up the lens. It's a cheap way for macros but not if you don't want to chance the lens.