If salt water, take the settlement and run. The salt will have all the electrics hosed with some problems not showing up for possibly years. Salt is nasty and will cause pretty much anything to corrode over time! Generally not worth it to try to restore it unless the bike is an antique or not replaceable. If the amount is too low in your mind, that is what your insurance commissioner is for. You can also get a lawyer. Also check and see if you live in one of the states that give you the choice of money or replacement (like the state I live in). Once the evil insurance adjuster knows that you are aware of that option, if it is available, they become mush easier to deal with. The insurance company generally only pays fair market value of the stock bike. If you have heavily customized (like fancy paint, extra chrome, engine mods, whatever) and did not have this stated on the policy, you were not insured for it, sorry.
If fresh water, wash the bikes, real well. Flush the tanks (radiator, gas and oil), drain the tranny and the engine of all fluids if possible, replace the oil (and cooling fluid) with what you normally use (don't go cheap just because you are going to flush it again), do a "major" tune up to the bike (plugs, wires and whatever else your manufacturer says to replace), treat all the leather with your choice of leather cleaner/conditioner. Replace any relays or "black boxes" if you have electrical problems. Also make sure there is no water in the lights or in the frame itself. Say a little prayer that they will start, then run the bikes until warm, flush the fluids (all of them all over again), refill and hope for the best...
As someone else posted, you may have problems with the leather stuff and some electric glitches if a sealed component was compromised down the road so be prepared for that.