That's a very good question. In terms of suffering most I'd say Caliban. That's because he has to live with the daily humiliation of being Prospero's slave on his own island. Unlike Prospero, Caliban actually belongs on this island; this is his home. If we could put ourselves in his shoes for just one moment, we'd most probably feel similarly aggrieved.
That doesn't justify all Caliban's actions, of course; his comical misalliance with the two bumbling idiots Stephano and Trinculo is a disaster just waiting to happen. But in fairness to Caliban, he only enlists the help of these clowns out of desperation. Being under Prospero's thumb is such an emotionally painful experience that he's prepared to do just about anything to see his master suffer.
Looking at all the characters in the play, I think it's fair to say that Miranda doesn't really suffer all that much. Though this is somewhat ironic given that in her very first speech she says, "O, I have suffered / With those that I saw suffer!"
With all due respect to Miranda, though, this isn't really suffering as most of us would understand it. Yes, she's genuinely upset at the sight of the shipwreck, but this is largely because she's been protected from the outside world and all its horrors by her sheltered upbringing on the island. She's therefore too naive to know what true suffering is. For the most part, Miranda is a passive character to whom nothing really bad happens. It would be pushing it to say that she suffers in the play.