You can sometimes get around red tape by installing a "temporary" dock. Thats what I did at my property here in NY once I found out I needed permits from 3 different gov. agencys.
I don't need ANY permits if the dock is removeable (I have to remove it for winter). I bought a shoremaster dock, very nice stuff. Good luck and keep badgering people until you get what you want. Eventually they'll let you do it just to shut you up!