San Pedro [1]’s got slim pickings in this category. The hands-down best is 
Ruby’s Hotel (tel. 501/226-2063, rubys [at] btl [dot] net, US$18–40), with 23 rooms in a building right on the water in the heart of the village. Ruby’s Café and pastry shop downstairs are excellent, and you can sit on your room’s balcony or the common deck space and watch the beach traffic below. There are rooms with either shared or private bath.
Your only youth hostel option is Pedro’s Inn (tel. 501/226-3825, www.backpackersbelize.com [2], US$12.50 s, US$22.50 d), with two rows of 14 wooden stalls, each with bed, ceiling fans, locker, and access to shared bath facilities. The rooms are right above Pedro’s Sports Bar and poker room, so you’ve got an on-site nightly social scene with a lively cast of characters and pizza available for delivery. Pedro’s has a small pool, deck, and shaded picnic area. It’s back by the airstrip (you’ll wake up to the morning’s flights taking off overhead), a seven-minute walk from the town center (or US$3.50 taxi). Across the street, Pedro’s has 30 functional hotel rooms for US$50–65 each with air-conditioning, TV, private bath, and fan.
Links:
[1] http://www.moon.com/destinations/belize/the-northern-cayes/san-pedro-and-ambergris-caye
[2] http://www.backpackersbelize.com