Well yes, a machine like this is plausible.
Others have stories about machines traveling to other starsystems, so I don't see why a "simple" thing like a storm generating machine would be unbelievable, if it is reasoned by future / further advanced technology than currently available.
But in order to defend the island, I would imagine it to be pretty ineffective.
Firstly, generating a storm needs time. If it just pops up out of nowhere it will be noticed, thus questioned, thus be looked into. As soon as this happens, more and more people will get aware of it and at some point swarm the place, as mankind is fixed on the idea of exploring and explaining everything. As a result you get exactly the opposite of what you've tried to achieve.
Secondly, even if the island owner is okay with the first one, a storm isn't able of defending at all. You would have to make sure, that the storm (or the thunder within) hits absolutely everyone / -thing approaching it. You could say something like shooting small balls of something, which are highly responding the the thunder, thus luring the thunder into following it, at the intruders. But then again, we already have machines hitting a speed of more than 2000 mph according to this wikipedia article. I doubt a thunder storm would reliably hit all of these things, if they'd raid the place.
And even if so, they could still go the underwater way, sending submarine to the island... Remember, it IS an island, thus in the middle of massive bodies of water.
And, as already mentioned in the comments of the original post, we already have satellites in the orbit, which should easily be able to spot every open building on the island.