The great news is that Whole Foods carries a very safe line of lunch box alternatives. All boxes are BPA free and the Crocodile Creek as well as Laptop Lunch bags are Lead Free.
Lunchbots: Stainless steel bentos including stainless steel lid, lids are powdered coated in different colors which help differentiate the size. They also carry the Lunchbots stainless steel liquid food containers, they appear to seal tightly. I do not own any Lunchbots, so I don't have an opinion about them either way. If you are looking for a stainless steel bento, this is a great route to take.
Find them: on the end cap of personal care, facing the new Bulk Department.
Next up, Tiffins which originated in India. We own a large Tiffin, I use for outtings with the girls and we fit all our food in one box (I love it). These Tiffins are personal size, stainless steel, and even come with a little mini container to transport liquids, like salad dressing. They are muli-tiered, to help separate foods, have little latches to keep them closed. They carry a 2 tier and a 3 tier Tiffin.
Find them: on the wall of the bulk department, lower shelves, on the other side of bulk spices.
Lunch Boxes, water bottles, small thermoses for hot liquids, and sandwich keepers. The lunch boxes are simple zipper bags, with an insulated type material on the inside, they also have a small pocket on the front. The sandwich keepers are obviously about the size of a slice of bread and is a nice reusable alternative to using plastic baggies. All made by Crocodile Creek.
Find them: End cap facing produce department near entry to bulk area OR end cap near last aisle of dry goods grocery, close to the wall of dairy. If you hit frozen cases, you've gone too far.
Laptop Lunches: Not sure if Whole Foods is phasing them out or just running low. You can find the insulated bags and replacement bentos with lids for the 2.0 system. The replacement "bento buddies" have one big compartment, one large box, and two smaller ones. They do not carry the large box that you store the boxes pictured below inside.
Find them: with kitchen utensils in the coffee aisle, once again, towards the frozen food cases, but closer to back wall where you will find dairy.