I have a 2006 Yamaha VX110 Deluxe. It sat in the water overnight and one of the plugs came lose filling the hull with water. The engine won''t turn over now.
I drained the hull, swapped batteries with the other jet ski (which works fine), cleaned the spark plugs (although there is still water coming out of the cylinders when I hit the starter without the spark plugs). What can I do to get it running again?
Just keep running the starter without spark plugs until everything drains? Anything else??

The first thing you need to do (immediately) is get the water out.
Next check to make sure your gas is good - drain and replace it if necessary, and force enough fresh gas throught he line to ensure there is no water there.
Next check to make sure you are getting spark at each plug - it will never start without spark. Then put in a NEW set of plugs and try to start it. It might just cough at first, or catch a little.
Then remove the plugs and clean and dry them. Replace them and try again.
You may need to repeat this operation multiple times, but it is important that you clean and dry the plugs each time, because they won't work wet.
Once you get it to run let it run at idle for a while to get any remaining water out.
Dave

How do I get the water out though?
I've heard of threading a tube down through the spark plugs to suck the water out, but is that the best way or is there some better way?

Just removing the plugs and cranking should get most of the water out. Was this in salt or fresh water?

Fresh water.

Good - fresh water is a lot less harmful, but you still need to get the engine running ASAP to avoid damage.