The best Borders store in New York [which means the best Borders in the world] was in the World Trade Center. They carried a selection of jazz cds that didn't rival Tower [no stores did], but was quite huge.
Regarding the megastores killing the independents, it wasn't the megastores, it was us, the consumers. If you/I would buy from the independents, they would still be around. One doesn't have to be a brain surgeon, to figure that one out..