I can't get into the ship.
When I get to it, there are two thugs that I kill. There are no other thugs on the dock and the door on the far side of the ship never opens. The thug that is supposed to come out on the upper deck never appears.
I've tried it with my 2 gang members (from Lizzie) and I've tried without them by leaving them behind.
Any ideas?

Hi,

Have you had a look at the video walkthrough on Youtube?

http://www.youtube.com/playlist?list=PL_mBx6OdgqWOKJd4cvcvdb16bV4bd52WT

Yes. I don't believe I missed anything.
I am replaying from my oldest save.

Hi,
You need to kill 5 casts to get the door open. 4 guys on the main deck and 1 girl on the balcony.

Restarting from an earlier save solved it.
I believe it may have been HMG ammo I had in my inventory.
I was flush with cash so I bought everything that the Pawn Shop would sell me. I didn't have the HMG but I purchased ammo any way.
The second time playing through I didn't buy it.

I'm having the same problem with the Pier level. I cleared out the entire place and can't figure out what to do next. I see a boat in the water but the water door is closed.

Edit:
I figured it out. I went to the wrong boat! It's not the small one, it's the large boat at the end of the level.