We stayed at the Best Western Marina Park which is now the Holiday Inn Marina Park in downtown right across from Bayside and the Port of Miami. Good spot for a pre-night. We also stayed at the Wyndam which is now the Radison. Both have port view rooms if you ask. The Raddison has a lot more rooms but is a min.or two further from port.
There are a lot of the major chain hotels around ,all just a few min. cab ride to the port.(Marriott,Doubletree,Hyatt,Intercontinatal)