This question is asked quite a bit over on the Thorn Tree forum and there doesn't seem to be any reliable way to go by sea.
But like ijkh said, there are loads of flights for under $350 r/t from MRU. I'm sure a boat would be a story-worthy experience, but I'm willing to bet the real fun starts in Madagascar so hurry up and get there!
(I'm Madagascar bound in October...can't wait!)