This has to be one of the most unique wedding destinations I can think of.  Underwater in Key Largo, Florida. 

The Jules’ Undersea Lodge in Key Largo, Florida is truly underwater, with guests having to scuba dive 21 feet beneath the surface of the sea and enter through an opening in the bottom of the lodge. The wedding ceremony itself is held inside the lodge, which consists of a wet room entrance area, two bedrooms and a common room, which is a combination kitchen, dining and living room area. The Undersea Lodge also serves as a memorable honeymoon location, with fish passing by your window.
Contact Info:

Jules' Undersea Lodge
Key Largo Undersea Park
Key Largo, Florida
phone:  305-451-2353
website:  jul.com
info@jul.com

I have several more unique wedding ideas on my website page at Unique Wedding Destinations.