What major metropolitan area in the continental United States has the smallest carbon footprint? It's Los Angeles, not ordinarily thought to be a mecca of energy conservation.
There are a few different things going on here, aside from the methodological caveats outlined in the article. One is that Los Angeles is simply less sprawling, and more dense, than most people realize (well, you might realize it when you're stuck in traffic on the 405...). In fact, this is true of the West generally: The region's popular image notwithstanding, it's the most urbanized part of the country, because rural areas simply can't support much in the way of economic activity. Ten of the country's fifteen most densely packed metropolitan areas are in the West. Since denser settlemement patterns reduce energy consumption, the West does pretty well on these measures despite its lack of a public transporation infrastructure--all but one of ten most carbon-intensive metropolitan areas are located east of the Mississippi.
Climate also contributes significantly here. Air conditioning requires much less energy than heating, so all else equal, warm-weather cities emit less carbon dioxide. (Honolulu is the only city in the country that beats L.A.) According to Wired, heating a typical home in the Northeast emits 13,000 pounds of carbon dioxide annually, while cooling a typical home in Phoenix emits only 900 pounds. And southern California--at least the part of it within about 20 miles of the coast--stays cool enough in the summer than even air-conditioning emissions are pretty low. Incidentally, this warm-weather advantage makes it even more remarkable that seven of the ten highest per-capita emitters are in the South, despite its mild climate. A heavy reliance on coal is partly to blame, but there's also a lot of low-hanging fruit to be had in terms of improving efficiency.