If you do decide to stay in Belize City, my recommendation would be D'Nest Inn. http://www.dnestinn.com/index.html
My son and I stayed there and it was fabulous! All things stated on Trip Advisor are a reflection of what a great place it is. If you do stay overnite, have them arrange for a 'ciyy tour' before you depart. Even a visit to the zoo is possible.
Jesse is correct also, if you are prebooked, and your flight is delayed Tropic will ensure you get to the island.
BTW I do my darndest to ensure I in Belize for at least a few days of the lobster season in Feb, and one of my most memorable meals with lobster was in CC. At the Sandbox and it was lobster lasagna.