I'm suprised that the cruise line doesn't have a coordinated tour package for you to choose land/sea tours from.
I live on Caye Caulker. Caye Caulker is 45 minutes via water taxi from the Marine Terminal, and Ambergris Caye is 1-1/4 to 1-1/2 hour. The Marine Terminal is located next to the swingbridge in Belize City. The price for water taxi is 15 bx one way or 25 bz round trip. Water Taxis leave from Belize City about every 1-1/2 hours, and return to the city every 1-1/2 hours. If you snorkel from Caye Caulker, you'll probably see Shark Ray Alley, Holchan and Coral Gardens. If you want to go to Goff's Caye, that is usually done on an all day manatee tour. You can email Carlos Eco Tours a reputable tour operator here on Caye Caulker at Cayegals@hotmail.com
Ambergris Caye has some awesome dive and snorkel sites, but since you're only in port 9 hours, to get to there in a timely manner, you would could take a taxi to Municipal Airport and fly over to San Pedro, a 20 minute flight, 84 bz round trip or 54 bz one way. Flying is much more expensive, but the ride is awesome, right down the reef and over Caye Caulker.