If you measure prestige in selectiveness and amount of money then NDSEG is the "better" award.
NDSEG
~200 awards, ~10% admit rate (http://ndseg.asee.or...the_application), and actually, for your field (Chemistry) the admit rate looks to be more like 6% (http://ndseg.asee.or...award_selection)
Tuition: Full for 3 years
Stipend: $30,500+$31,000+$31,500
NSF
~2000 awards, ~15% admit rate (www.wpi.edu/academics/FS/nsf.pdf)
Tuition: $12,000 tuition/yr for 3 years
Stipend: $30,000/yr stipend for 3 years
Obviously, it's an honor to get either, so congratulations!
EDIT:
This post from last year has a better-explained breakdown of the differences between the two. Bottom line: it'll depend on the funding structure of your program, your particular field of study, and your own preferences.