Yamaha has the best reputation among cruisers, and the best worldwide distribution. Nissan also makes very good and reliable engines but they are rare in out of the way places. My friends with Hondas complain about them being hard to start and expensive to fix.
Alway choose the biggest engine you and the boat can physically handle, but watch out for the weight of new 4-strokes. They are much heavier than an equivalent 2-stroke.