The short answer is that, rather than comparing one to the other, use BOTH for proper cleaning!
When flossing, you go between the teeth and under the gums to remove excess plaque that cannot be removed by simply brushing. It is recommended to floss at least once a day.
A Waterpik cleans the gums and teeth in a similar, yet different way than floss. It uses a high-pressure water stream to push the gums back and remove any traces of plaque. Both of these items are powerful for cleaning teeth and are best used together.