I did the exact same thing. Normal puddle on the side of the road, drove through it and water sprayed up into my intake. Got about a gallon straight into the intake and shot a rod out the side of the block.
As for repairs, mine was covered under comprehensive insurance, but I believe the bill for a used motor with 45,000 miles installed with all new components (water pump, spark plugs etc) was $4500 from a local shop. If you do the work yourself, expect to pay around $2000 for a good engine and then add a few hundred for new parts. Another tip is to be very careful when buying an engine, as there are a few different 1GR'S that are very similar. I got the wrong engine three times and it took the Toyota dealer over a month to figure that out.
Good luck, I know how much this sucks, such a harmless puddle that can do so much damage