Typically there are at least 2 days a week with no ships in Belize City so plan your mainland tours then. Most tour operators know the days. A couple of smaller ships still offered a tour to Ambergris last year - don't know if that will happen again this year. The impact was alway very minimal with only a couple of dozen cruise shippers touring the island for an hour or two. Local tour operators do get busy with overnight guests so it's not a bad idea to line up your tours ahead of time or as soon as you get in. Fishing can especially be hard to book last minute in the high season.