I'm not sure this is ever addressed in the books, but would chocolate made by Muggles work against the effects of Dementors, or would only wizard/witch produced chocolate have an effect? Why or why not?
It's not addressed directly in any of the books or JKR as far as I can find. That said, I think there's an argument for the existence of magical chocolate.
I think it's possible that wizarding chocolate may contain a magical component. That said, if chocolate does contain a magical element, we can't automatically assume that the magical component is what actually counteracts the Dementors. I think it's highly probable that any magical element in wizarding chocolate would indeed be what counters a Dementor's effects, though.
In Order of the Phoenix, following the Dementor attack in Little Whinging on Harry and Dudley, chocolate isn't even brought up -- not by Harry, Arabella Figg, Mundungus Fletcher, Arthur Weasley, Dumbledore, or Sirius. Perhaps it was because Harry had no access to wizarding chocolate; it could be that Muggle chocolate -- all that Harry would have had access to at Privet Drive -- was the wrong kind of chocolate to treat a Dementor attack with. (Ironically, in Order of the Phoenix, Harry threw away two boxes of Honeyduke's chocolate before the Dementor attack because he was feeling angsty and mad that no one was contacting him)
There is canon premise for magical ingredients being used in sweets. For example, Billywigs (FBAWTFT¹ page 4) are Australian insects that cause a pleasant floating sensation when they sting; Billywigs are the active ingredient in Fizzing Whizbees. The Glumbumble is a grey, furry-bodied flying insect that produces melancholy-inducing treacle, which is used as an antidote to the hysteria produced by eating Alihotsy leaves (FBAWTFT page 19).
Blending potions has a magical aspect it to it. Perhaps wizarding candy is similar and does too. It seems unlikely that Lupin went into the Muggle world just to procure Muggle chocolate, even less so that Madam Pomfrey would have (she had chocolate on hand in the hospital wing in Prisoner of Azkaban). Dementors are of the magical world; it would seem that to counter their effects would require some kind of magic (whether that's the regular chocolate, a magical ingredient, or both).
So, do we know for sure counteracting the Dementors requires magically-produced chocolate? No. Is it a possibility? Yes.
¹Fantastic Beasts and Where to Find Them - Newt Scamander - Scholastic Edition
I don't think there was ever any implication made that Lupin's or Madam Pomfrey's chocolate was a special "wizard" chocolate - it was therefore likely a regular unenchanted muggle chocolate.
As noted in the comment by gnovice, this question explores the reasons why Muggle chocolate might work: Is there a scientific basis for the healing properties of chocolate?
No mention of chocolate in that context in any of JKR sources.
There does not seem to be a need "wizard-made" chocolate... The chocolate itself is magic (1)!
The mood-enhancing properties of chocolate are well known in both the Muggle and wizard worlds. Chocolate is the perfect antidote for anyone who has been overcome in the presence of Dementors, which suck hope and happiness out of their surroundings.
Chocolate can only be a short-term remedy, however. Finding ways to fight off Dementors – or depression – are essential if one is to become permanently happier. Excessive chocolate consumption cannot benefit either Muggle or wizard.
(1) By magic, I mean the power to make one feel better is the chemicals it naturally contains!