Upvote:3
Unless things have changed since I last looked at this (and it's been a few years), your only option is to fly. In these days of low cost carriers, it may also be cheaper to fly via eg. Kuala Lumpur on Air Asia, even though this makes no sense geographically.
And for why there are no ferries: the southern Philippines (Mindanao) are strongly Muslim and in parts little short of a war zone, while northern Sulawesi is strongly Christian. There's thus less cultural connection, and consequently less demand, than you'd think from the distance alone.