What's your performance space like?  Can you give us a description and/or some dimensions?  Do you have a goodly bit of wing space available?  Can you fly scenery in?

The island, I wouldn't actually build much.  Use a drop of a tropical island.  Build palm trees on trucks, wheel them on and off stage as needed.

The pirate ship I'd not build fore and aft sections, although, if you're going to do a side view, possibly consider building the set on a bit of a rake, to really get the sense of the shape of the boat.  Me, I'd build it as if I was looking at the boat head-on -- that gives you at least one higher deck, stairs on either side of it.  One door to the area below the upper deck (I really don't know nautical terms, sorry.) , and the entire floor to use as the main deck.  Or, build the upper deck on an angle rather than straight on, and also cart out a masthead on a small truck to delineate the front of the boat.  You can fly in the bottom side of the mainsail and some drops resembling rigging...
 
(I'd sketch this out, but I can't find a pen. :( )

For our version of "Pirates" we had just the upstage bulwark/ship's rail - freestanding in sections on an A frame, then had a bow section for the anchor/etc. on casters, a mast made of tubular concrete forms and flown up & out, a 7' tall wagon as the "poop deck" with the ship's wheel on top and ship's ladders leading up to it (a door in the side as well) and a bannister around the top area for safety, and cargo nets/ships' "rigging" ropes flown in from above.  We had some props on the deck like trunks, ropes, and a "deck hatch" on a 4x8' wagon.  This "cutaway" left the whole downstage area for the "deck" for acting and went onstage/offstage pretty quickly.