The Merry Go? Well, you could presumably camp out in Chopper's cabin- he's a canon, he's small, and Sues don't usually attack him. From there you can pull a 'invisible handmaiden' thing, like in TOS.

Alternatively, you could always just approach Luffy and ask to join the crew. He'll most likely say yes unless he's so far gone that he might as well be an OC, and if any OCs catch you, then Luffy can vouch for you being a crew member.

This, of course, depends on the crew actually landing somewhere. If the fic starts out on the ocean, I'd just portal to wherever they're going to be landing, and take the charges from the Words.

If they're going to spend the entire story on the ocean, then you're going to have to actually have to hide somewhere, and my only real suggestion is the kitchen that presumably exists, since no one ever bothers to think about it.

In plain sight. Cargo bay is a risky possibility, but the fact remains you have to find a way to feed yourself and find water. If your in the ocean, chances are people will notice if it goes missing, and there will be a search.
If they are coast hugging, it will be rather easier, but on a small ship you will likely have trouble. As they are pirates, there is likely a hidey hole beneath the floorboards or in a similar hard to discover area where they keep valuable cargo, but it depends how often they check on it, and the aforementioned issue of supplying yourself.
All in all, I would recommend your best chance is some sort of disguise. If you can't make them open up to you, pretend to be someone they can't dislodge, either out of fear or respect.
- It is a tough question.

I dunno. But really there shouldn't be much of a problem as long as nobody actually runs into the agents and they're not being excessively loud, due to the cloaking effect of the SEP field and the canon being helpful.

I like the small disguises idea, though. If ridiculously large disguises can be done (e.g. dragons), then there's no reason ridiculously small ones (rats?) can't. Plus, massive potential for humor in trying to use equipment which may or may not also have shrunk, not be stepped on, etc.

~Neshomeh

Maybe you could disguise yourself as something inanimate, like a barrel? Or you could somehow shrink. Smallness is the next best to invisibility, for stealth.

Best I've got off of the top of my head.