There's a few of them that I like- I love GMD prefolds and while I haven't ordered directly from their site, I wouldn't be opposed to it since many people have good experiences with it www.greenmountaindiapers.com
These are my go to's when I need something:
but my absolute favorite (I know, I say this all the time ) is http://hyenacart.com/BetterBums/ because D's diapers are just awesome and hold up so well through the years and, well, yeah..she's awesome to work with too. I could go on and on forever about her.
I was going to link you to BSRB's too b/c I love them but I'm really out of the loop an apparently they've closed but this site is also good and the mama is GREAT to work with http://hyenacart.com/mandismenagerie/