I've only been to Carnaval in the northeast of Brasil but have been in Rio just preceding the start of it. Carnaval is a great time to visit Brasil but I think that Rio, because of all the international visitors, becomes more commercial and expensive. Also, it becomes more dangerous and the chance of being taken advantage of becomes greater. If you have accomodations on board and travel with groups I think it would be a wonderful experience. Since Carnaval lasts a week (with precarnaval activities) maybe you'll get lucky and the ship will stop in Bahia before Rio.

Have a great time.