There are a number of options when it comes to touring the Tonle Sap lake.
Beyond Unique Escapes beyonduniqueescapes.com. This operator offers excellent value, excellent service, guaranteed departures and small groups, with tours to Kompong Phluk (or Kompong Kleang during the height of the dry season).
Osmose Nature Tours osmosetonlesap.net. Insightful lake trips run by this local NGO who specialize in the Prek Toal area of the Tonle.
Tara River Boat taraboat.com. The main tour operator for the lake, offering half-day tours on their big boat around Chong Khneas, plus sunset tours with free meal and unlimited drinks. They can also arrange trips to Kompong Phluk, Kompong Kleang and Prek Toal using smaller boats. Tickets for most trips can be bought from hotels and tour operators in Siem Reap.