We did both boats last year when going to MK from WL. The larger boats go directly to MK from WL but they are not as frequent as the smaller boats which go to CR, so one time we took the smaller boat over the CR and then walked to MK.
We also took the smaller boat to CR and then took the monorail to Epcot. It was not the quickest way to get to Epcot and maybe not the easiest if we had had small kids, but it was way more fun than the bus.