Read the terms of the warranty that you signed and determine how "driven in water" voids it, confirm the process by which they determined your warranty is void, get answers in writing on an official letterhead. It's one of the oldest tricks in the book to declare a new car's warranty void for any reason they feel like.
If you forded deep water and submerged the transmission and the denial is valid, get a quote from Suzuki for a proper diagnosis, parts and labor. Being out of warranty doesn't mean they won't accept payment to perform the repair. And if the transmission was submerged, it likely won't be just the throwout bearing that needs to be inspected, so get a full confirmation of the issues that need to be addressed.
