1)Geographically, Boulder is pretty darn perfect for running. Altitude, weather, availability of trails, etc. Few other towns in the US fit the bill - Colorado Springs, SLC/Provo, Flagstaff, Eugene, a few pockets in NoCal and SoCal...this point cannot be understated. Living in a place like Boulder is inspiring for runners of all ages.
2)Culturally, Boulderites are far more likely to lead healthy lifestyles than those elsewhere in the US. You don't move to Boulder for it's robust manufacturing industry, the nightlife/clubbing scene, or for the shopping. You move there for the limitless outdoor opportunities. As a previous poster said - fast people are having fast children in Boulder.
3)Niwot and the larger school district, not only allow but encourage open enrollment from all over Boulder County. Families have a lot of freedom to choose where their kids get to go. It's not some sort of taboo like it is in other parts of the US.
4)Niwot's off-season club (it's much bigger than just Niwot now), REAL Training, offers youth/MS programs as well as very robust off-season programming. If you're attending a neighboring HS, it's highly unlikely that the HS coaching staff at many of those schools is willing and/or able to put as much time into summers and winters as those at REAL. Kids that love running find a match with the REAL/Niwot program and gravitate towards it.
5)Christensen (and the rest of the staff at Niwot) knows what he's doing and kids like him.
The only thing Niwot HS does not having going for it is its size. ~1200 kids is significantly smaller than the Yorks, Great Oaks, Woodlands of the world.
Until another Boulder-area HS program is able to compete with REAL at point #4, then Niwot will continue to have national-level success. Even if another program can build something that dilutes the Niwot pipeline, there's still enough talent in Boulder Country to support multiple elite HS teams.