Both are good cameras to start with photography. I had a similar dilemma to yourself where I was choosing between the D3100, D5000, D200 and D90. In the end I chose the D5000 along with 18-55VR combination (I already have a Sigma 15-30mm, Nikon 24-120VR, Nikon 50mm 1.8 and Tamron 70-300).
I based my decision on the reviews here on DPreview.com It got a good solid 75% rating and the only real downside of the camera for me is it has no Internal motor so lens choice and auto focusing is a little limited.
I also intend at some point to get the 16-85mm VR as my walkabout lens so I'll probably end up getting rid of the sigma 15-30, Nikon 18-55 and Nikon 24-120VR as 16-85mm covers 90% of my photography needs.
I think the D5000 with both 18-55VR and 55-200VR will cover probably most of your photographic needs especially if it's your first DSLR.
Both cameras are fine though and you'll be happy with either one