Chipotle's Mexican Grill
I have never been, but Chipotle's has a list of allergens on their website that basically makes their restaurant a great place to visit. I am g-f and dairy-free, and their website says that there are only 2 items that even have dairy in them on their menu.
They also appear to have a soft tortilla that does not contain wheat.
My son has been dying to go here, so I know this will be a place I will try soon.