Try ecohaus in San Francisco. They have several lines of 100% natural comprised of wool and natural latex) and non-toxic carpeting: http://www.ecohaus.com/C-42/carpet
Flor is also a good option. They're carpet tiles you can arrange to form an area rug or lay out to cover an entire room. They're made from recycled materials, emit very few VOCs and don't require glue. Another bonus, you can replace just a tile or two if there's a super stain you can't get out: http://www.flor.com/
If you do go for conventional carpet, ask the company to store it in the warehouse to air it out for a couple of days before you have it installed. After it's installed and for at least three days, open your windows to let the fumes disperse. They're pretty toxic.