Seadoo xp. They're the largest engine stuffed into the smallest hull they made in any given year.
$1000 is doable. Tough, but doable.
Also, expect to wrench on it. Probably quite a lot.
Oh, and apparently the '96 model is favored over the earlier ones. I have a 93 though and it's a blast. Really retarded color scheme, but I don't care.
I keep thinking of more stuff to add to this.
If you get a two stroke, and you probably will for that price range, I'd HIGHLY recommend doing away with the oil injection and converting it to premix.
For the not so mechanically inclined, two strokes use gas mixed with oil. Premix is, well, oil mixed in with the fuel, whereas oil injected is generally more convenient. You add pump gas in the gas tank, and the oil is added to a different tank that automatically mixes it with the gas before it runs through the engine. The problem with this is that on a boat that's at least a decade old, the oil injection system might malfunction, and you'll end up fucking up the engine.
That's all I can think of for now.