I think I may have figured it out

pygments.lua

@@ -0,0 +1,12 @@
+function CodeBlock(block)
+  if block.classes[1] == "moon" then
+    local fname = os.tmpname()
+    local handle = io.open(fname, "w")
+    handle:write(block.text)
+    handle:close()
+
+    local p = io.popen(string.format("pygmentize -f html -l moonscript.py %s -x", fname))
+    local out = p:read("*a")
+    return pandoc.RawBlock("html", out)
+  end
+end