Yes, you can but the people who were going to 34th had to switch boats at Pier 11 this morning.
My feeling is that it is probably better for business, for those going to midtown or anywhere west of Madison, to get a subway downtown and continue the commute that way.
The alternative is to switch boats at Pier 11, then get on a crosstown bus at 34, and then get whatever subway you need to complete your commute.
Folks that work in midtown can avoid that mess by taking the ferry to Pier 11 and then walk over to Whitehall for the N/R, or Wall Street for the 123/45.