My list of the top Maya sites in Belize looks like this:
1) Caracol, Chiquibul/Mountain Pine Ridge
2) Lamanai, Orange Walk District
3) Xunantunich, Cayo
4) Altun Ha, northern Belize District
After that it's a little hard to rank them in terms of interest to the visitor. Certainly Che Chem Ha or one of the other cave sites would be on the list, along with Lubaantun near PG and several others.
Of these, Lamanai and Altun Ha are the easiest to visit on day trips from San Pedro. I'd personally go to Lamanai. The trip there on the New River is great, and the setting along the New Lagoon is beautiful. Also, you will see howler monkeys at Lamanai, which you won't at Altun Ha.
Belize First Magazine http://www.turq.com/belizefirst/