Swimming is way better to work out, because your body makes a bigger effort. Running is good too, but you'll end up working out the legs, while the rest of your body is not very developed by that.
You're right there and swimming does provide more of a full body workout that running does, even though I still don't think it competes with cycling.
Cycling can also work out your whole body, and a lot of people don't realise that, and just think it's your legs that are working, but that isn't the case.