If you're looking for reproduction Post War Lionel boxes, yes there are vendors who sell licensed Lionel boxes.
http://eastcoasttrainparts.com/
If you're looking for plain corrugated boxes, I use "trading card" (to us older guys, baseball cards) boxes. They are sized according to the number of cards you can fit in a box (550, 660...) or shoebox style with multiple slots. I buy mine from a local memorabilia shop that sells trading cards as well. Like these:
http://www.comicsandcardsuppli...ding-card-boxes.html
Hope this helps.
Mike