I can achieve this behavior by just modifying here

   const printer = createPrinter({ newLine: NewLineKind.LineFeed });
-  let output = "";
+  let output = "// Code generated by sqlc. DO NOT EDIT.\n\n";
   for (let node of nodes) {
     output += printer.printNode(EmitHint.Unspecified, node, resultFile);
     output += "\n\n";
   }
   return output;

But I'm not sure if it's OK or should be handled in another place.

Might be better off somewhere that has access to the configuration, so that a user can either turn that comment on or off or can supply their own header, like a copyright string.

The Go code generator adds the header by default and you can't turn it off. I think it's a good idea to always add it.