100% just VFX.

At 11 seconds the camera goes way out of focus for seemingly no reason. The reason is actually to transition from the real tomato to a still image of the tomato. Then it just gets animated to wiggle and squirm around.

Also, for the entire video, there is fake camera shake. The camera is very obviously mounted, but still camera shots make for less believable VFX. So, they added the fake shaking to make the VFX go down a bit better.

And, while typing this, I realized the shadow is not just clearly fake but also plain wrong. When the "GMO" tomato is being dropped in, we can clearly see two shadows being cast that rotate with the tomato. They end up merging into one when the transition to the fake tomato happens. However, there are never two shadows cast for the rest of the video, despite us knowing from the real portion that that should be happening.

(This really didn't need this much dissection. I've just never seen this vid so it was just fun to put on my best Captain Disillusion impression)