Change your oil and plugs first. You probably have water in the crank case if you sucked water in it. That will make you knock, and can foul plugs very quickly. Sucks you just had it done...

If it persists, your bearings are hosed, and $250 isn't that bad of a deal. I'd be surprised if the plastigage would be accurate without removing the motor, disassembling it, and running it through a parts washer. You need to do a dry assembly for plastigage to be accurate. You might want to pay the extra $100 to go through a dealer so there would be some matter of liability on their part.

If anyone ever has this happen, the first thing you should do is quickly pull the plugs and the MPI fuse (fuel injectors), and crank the engine for 30 seconds. You'll eject the water out the plug holes and exhaust without putting any pressure on your internals. If you don't pull the MPI fuse, you cold start a fire because fuel vapor will spray everywhere.