It all lies with friction or contact or drag concept . A Hovercraft slides over or above the water with less contact with the surface (water) due to air cushion so it has less resistance in moving . where as the boat or speed boat has no means of flying it has clinch and to peal the water so it has much contact and also the propeltion system is not efficient as it is with hovercraft.
Its because a water boat has a propeller which is underwater whereas a hovercraft has a large propeller above at the back and pushes with the force of the wind. A hovercraft has a cushion filled with air which lifts the hull of the craft  thus, decreasing friction and resulting in faster speed.