I'm pretty sure physics don't work that way, and I'm dead certain that without a thorough analysis of his experiment - including the control conditions - that's a heck of a claim to make.
It's not so much that it's a scam as it is pseudoscience. There are a lot of things that can be said about energy and resonance, but you can't make rice rot based on positive or negative thoughts. That's caused by bacteria and fungi, not the vibrations of the water, meaning that either one jar had purer water than the other, or one jar was sealed more tightly than the other.
That's not to say that manifestation isn't real, nor is it to say that you don't get back what you put out. But that has more to do with the emotions of those around you and your own personal success - the more positive you are, the more apparent that is to the people around you, and the more likely you are to succeed. The more negative you are, the more apparent that is as well, and the more likely you are to fail as a result. I don't think anyone has been able to do a realistic experiment on how your emotional output affects the vibrations of the particles around you, because human emotions are so subject to change that it's almost impossible to get a control base for it (in other words, finding someone that would be consistently neutral and not likely to be distracted by any other thoughts or emotions for the duration of the experiment).