How about boat trips? We did Lamanai twice from Belize City. Yes there is a bus ride, but not too long as I remember. Then a fairly leisurely boat ride up a narrow river full of wildlife to the magnificent Mayan ruins. Boat trip and bus ride back. We loved it enough to take a friend back there.
Again at Santo Tomas we took the paid trip up by speedboat and then by a slower boat up to see the Maya refugees who live in the Qe'qchi village. It also, back then, included lunch in the town of Livingston, a Garafuna town which was also very interesting. The speed boat ride was a bit harrowing, take a hat with a strap or otherwise cover your hair!