In the comments section of my last post, Cap'n Transit points to an entry on his blog that brings up an aspect of making connections to the ferry that I had not considered. Namely, that the ferry companies do it. The Cap'n mentions the success that New York Waterway (the "Jersey ferry") has had with running shuttle buses both in Manhattan and New Jersey. Imperatore and company figured out long ago that without connections on the land side, ferries were really only useful to people who lived and worked within a short walk of the ferry. By providing an extensive shuttle service on land, NYWW has greatly expanded its customer base. By doing so, they effectively eliminate the need to get on public transit in Manhattan, thus eliminating the two fare problem (in the process, though, adding to the congestion on Manhattan streets).1

I'd recommend reading Cap'n Transit's original blog post (Water Taxi: What If?). He also touches on the issue of accessibility that I discussed, but from the point of view of LIC commuters. The formula remains the same (live near the ferry, work near the ferry - no problem), he just provides more and different examples. The rest of the blog is also worth a tour.