You don't really need reservations to fly to San Pedro on Tropic or Maya Island, as they have flights all day long from international (and cheaper flights from muncipal, worth looking into if you're traveling with several other people). But, it doesn't hurt to have them. Usually your hotel on San Pedro can make the reservations for you at no charge to you.
Yes, there are ferries -- really, more like water taxis -- from Belize City to San Pedro. The most reliable in my opinion are the Caye Caulker Water Taxi Association boats, fast open boats with twin outboards, which leave at 9, noon and 3 from the Marine Terminal (US$12.50 one-way, 1 1/4 hours or so). You'll have to pay US$17.50 for a taxi into town, from the international airport (that's for the taxi, not per person).
Belize First http://www.belizefirst.com/