I usually stay at either the Holiday Inn Bayside (used to be the Best Western Marina Inn) or the Sheraton Biscayne Bay. Both are close to the port ($5 taxi fare). The Holiday Inn is a budget property, but is directly across from Bayside Marketplace so the location is perfect. Rooms are standard Holiday Inn rooms (satisfactory but nothing special). If you are looking for something a little bit more upscale (but usually more reasonable rates then other properties in its category) - go for the Sheraton.