I really dislike dl64 against Fox. He can camp you to no end and moves around much better there than Samus can. It might be beneficial if you play as a patient Samus, but there's really not a good way for Samus to catch Fox there, and it doesn't really have any disadvantages for him.
As for an actual counter for him, it'd have to be one of the non-neutral stages, but I don't have much experience on them myself, but I'd suggest Brinstar or Old Kongo Jungle. Old Kongo Jungle for the reasons blowtoes said, although the tall outside platforms are good for Fox. But yeah, if you're good on that stage, the fact that he has few recovery options (since to make it up to the upper platforms he'll do his upB where you can missile him) might be enough to win the match. As for Brinstar, I just do it since it has acid and he's a FFer. :/
And I guess it has almost the same thing with his recovery, but you can't missile out from the stage, and there wouldn't be as much of a necessity for the Fox to be at missile-level either. (thinking out loud [text >_>])
Does anyone play on that stage much? I've CP'd it a few times but haven't figured out if it's actually a samus stage or not. I do remember the no missiles off of the sides from the ground being rather annoying, but that was when they were all I relied on for edgeguarding lol.
Cstick in the air is good for falling through platforms with a uair, then FFing it, since it's more difficult to do with the control stick, and getting a random jump while trying to fall through a platform isn't exactly desirable. But yeah, it's all preference and you're not missing out on much.