I wouldn't. buying refurbed is always a gamble even from a reputable dealer, and considering the frequent lack of warranty, it's really not worth the (usually minimal) savings.
As for lenses; the most important criteria are what can you afford and what kinds of pictures will you be taking (will you be shooting indoors, close up, far away, shooting sports etc.). for most people the best all around lens ends up being some sort of standard zoom lens. Be sure to stay away from those cheap 18-55mm compact lenses though, they are absolute Junk. Also stay away from these super zoom jobs with the huge focal range, image quality is usually poor and they tend to be cheaply made (a zoom lens really shouldn't have a range greater than 5-6x).
beyond that, look for things like internal focus motors (AF-S lenses with nikon), some sort of image stabilization (VR for nikon), metal lens mount (plastic lens mounts are a good indication of cheap construction), internally focusing (lens doesn't get shorter or longer when focusing).
D90's come in a kit with an 18-105mm lens which should be pretty good, but if you're planing on buying your lens and body separately, I'd be more inclined to go with their 24-120mm (the 24-120 is internally focusing, the 18-105 isn't).
as for places to buy, amazon is aways good, as are these two:
http://www.adorama.com/
http://www.bhphotovideo.com/
(I prefer B&H myself)