The two best ways to travel from Puno to Cusco or vice versa is by either train or bus, depending on how much money you want to spend.
Peru rail offer a service called the Andean Explorer which is a first class train service and costs $220 per per person one way!! The journey is 10 hours! Alternatively there are tourist bus services provided by Inca Express and First Class busses, and you can travel each way for around $30. Journey time is about 8 hours with tourist stops en-route.
Or finally you can just take a normal bus, I reommend Cruz del Sur, as they have great modern busses and are safe. One way ticket is about $20 per person.