Try the Tropic Air tour to Lamanai.
You fly to Tower Hill airstrip(15/20 min flt). Take a short ride to the New River. Take a facinating boat ride down the river to the ruins.
Get to spend a couple of hours at the ruins with very few other visitors. Then back to San Pedro. You are back here around 1:30.

What makes the trip worth it is that:
1) You don't have to travel boat, bus, boat for at least 6 hrs (1 hr only at the ruins with alot of other visitors).
2) Best of all, you miss the cruise ship visitors.
They arrive at the ruins as you are leaving.

Tropic Air offers other tours, but I am not familiar with them.