GameReproductions used to be really good, but the last time I looked their supply of SNES games were dwindled quite a bit, and their Sega games were as well. Maybe this is due to the aforementioned chip shortage?
RetroQuest is a fairly new site though (it's who I got from Shin Megami I and II from), and while the main dude's English may not be top notch when you talk to him, he can create any custom ROM carts for you, including box and artwork. Customer service was also good - he asked me to please try the games out when they got to my house, and was happy to comply with my requests to send a picture of the carts, the box, and the actual game playing on a SNES before he mailed them to me. I can verify that the two games I got from worked very nicely too, so you may want to see if he can help you with your specific needs. If you want to see the carts I have, let me know and I can snap a few pictures.
Finally, Warners Retro Corner is around, but I've never worked with them so I can't personally comment on customer feedback or their site's friendliness.