How many hours do you have on this "brand new" 2010 boat? What is the warranty period and I am assuming that was an additional 3 year add-on?
Did they have any idea how the water got into the engine? Was it an issue with the cooling system, or water in the bilge? I would assume they must have thought water in the bilge enterered the air-intake?
Any previous SeaDoo boat dealer should have the ability to order the actual tower used on the 2007 Speedster 200 Wake model. That would be a starting point to find out how much the OEM tower was worth. All parts are listed on the SeaDoo website under parts right down to the tow mirror and grommets for wiring.