Not sure of the cause just yet... There seems to be a lot of confusion about what happened...
Fire in whole foods. Not a single person including us took the alarms seriously until the sprinklers came on... twitter.com/jameschororos/…— James Chororos (@jameschororos) January 13, 2013
BoweryBoogie has collected information here.
More information as it becomes available...
You may have heard there was a fire at Bowery - luckily it was small & all are safe. The Bowery store will reopen very soon, 30 min ETA— Whole Foods NYC (@wholefoodsnyc) January 14, 2013
Gothamist has a video from inside the store here.