I don't think you would be wrong to go with either of those bodies. Both have an auto feature, for point and shoot mode, but will allow you full manual control when you are ready.
As far as lenses go, the 18-55 is a nice walk around lens but won't really allow you to get those great close ups you see around here. You would need a macro lens for those.
I got the 18-55 and 55-200 as a kit with the D40 body for ~$650 and couldn't be happier. (Well, I could be if it came with a macro for the same price. And a nice tripod too.) The two lenses give me enough reach for now, and I can get decent pics of my tank too. If you can find the VR version of the 55-200 in that same kit, do it.
If you are set on Nikon, which I hope you are(being a Nikon guy), check out Nikonians.org for lots of other info/help/etc.