The Stahlratte seems to be highest rated but OH SO EXPENSIVE. I've heard of at least two other boats making the run. Look on ADV Rider in Latin America section. The boat captains sometimes post there as do clients.
Also there is a new Ferry running ... but it's of dubious reliability. Not sure it's in regular use or not. If they can get it together, this could end up being the cheapest option. As of now, mostly NEGATIVE comments on the Ferry. Lets hope it will improve.
If you are really adventurous, you can hire small "launchas" (15ft to 20ft outboard powered boats) These guys have to island hop and have to avoid open Ocean. This has been done, but really uncertain. Hundreds of routes in and around hundreds of islands and waterways. I did read a report on this. It took the guy about two weeks, 4 or 5 different boats, about $300 total cost. This was 3 or 4 years back.
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