It would appear that the dealer has indeed quoted you an amount of more then the car's book value, probably in attempt to make you go away... they probably are afraid of a vehicle with water damage to electronic components continuing to come back after they have worked on it due to other electronic problems.
If the vehicle was in enough water to get the seats wet, it might be a good idea to have the transmission fluid changed and any other components below that level checked for water intrusion damage (at some repair shop other than the dealer).
If the information I have provided is helpful, an accept is always appreciated! thanks!