The most common transport from Ko Samui are tour boats taking 40-50 people, with lunch on board. These require you to transfer to a longtail boat to get onto the shore of whatever island you are visiting, which can be tricky and requires a modicum of fitness.
Or else you can take speedboat tours which also provide a snorkeling program and less people in group/board. It gets you to the archipelago faster. The best way is to put together a group of friends to hire a boat and explore the islands and beaches in your own time.
Most tours go to the Park's Visitor Center for lunch and kayaking. The Visitor Center is visited by most tour operators, making it very crowded. This applies for the time from about 10am to 4pm. Before and after it's a totally secluded place with almost nobody around.
