Don't rock the boat! Stay away from my ship! You'll be better off if this world you skip.
My sister is right. This is the hardest world in the game, but with my help you'll do just fine. To get to the puzzle, you must first transform into the pumpkin and make your way out of Mad Monster Mansion, towards the small shed in the back. Break the coffin and pound the switch in there. Now, make your way past the 450 note door, and into the tunnel on the left. Swim to the highest tunnel and the puzzle will be in there. On the way you passed the entrance, so simply backtrack.
To me Tooty's beauty will soon go, to make me as pretty as that Leonardo DiCaprio!
Jiggies
Smokin' - Climb to the top of the smoke stacks.
Wistful Thinking - at the wistles at the front of the ship, pound in the code 312111.
Captain - Break the windows on the side of the ship to get into the captain's chamber.
Windows - On the large grey sheds, break the windows that face upwards. Go inside and navigate the boardwalks to get the jiggy. If you fall you'll have to swim out and start over.
Fan Letters - Near the back of the ship, jump down the pipe that doesn't try to bite you. Pound the switch inside. Make your way to the door on the smokestack, and beak barge it open. Make your way through the fans using the wonder wing, carefully timing your jumps, to the jiggy. This will take several tries, so do it either first or last.
Danger! - Inside the smokestack (where you got the above jiggy) pound the two fan switches. Race to the back of the ship, jump off, and grab the jiggy. Get out of there quick and to the box out back.
Crane-ky - push the up button on the crane closest to the front of the ship. Race to the jiggy fast.
Boss Boom Box - go to the other crane, push the down button. Jump down the hole it makes. Kill the boss Boom Box either with a full supply of eggs, or a full supply of gold feathers and the wonder wing move.
Dolphin - swim into the anchor hole on the back of the ship and go in. Make your way to the back and pound the switch.
Jinjos - One's in the middle blue box (in a series of three). The green one's in the toxic green pool; makes sense, doesn't it? One's past the eight egg toll bridge. The pink jinjo is in the hole in the mesh grating near the ship's stern. The yellow jinjo is on a barrel in a pool of water, gaurded by Snacker (the shark).

Notes
5 - gang plank
6 - stern of boat (11)
12 - gang planks between funnels (23)
2 - on steam siren house (25)
5 - in galley (30)
4 - around beehive on dock (34)
4 - around turbine switch (38)
5 - in room with pipes, from ventilator (43)
5 - on rim of shark pool (48)
3 - in toxic waste pool (51)
12 - in container crates (63)
4 - in flooded warehouse (67)
6 - around base of cranes (73)
4 - in anchor switch room (77) *
4 - bunk room (81)
4 - chart room (85)
3 - captain's cabin (88)
12 - engine room (100) *
(* most difficult to collect)

Extra lives
One's in the right side blue box.
One's in one of the big grey sheds.

Extra Honey comb pieces
#1: Inside the hexagonal cove in the entrance to the big smoke stack.
#2: Swim through the hole in the plaster where the Snacker and the yellow jinjo are.

Witch Switch
Climb to the crane's arm (the one you push downwards, above Boss Boom Box's chamber) and jump for the large grey tower to Banjo's left. The jiggy that appears is obvious.

Valuable Tip
Just swimming on top of water takes air, and swimming under the water takes double air. Also, outside of the Rusty Bucket Bay entrance, there is a box with the Rare logo. Beak bust it and the switch underneath of it.