In addition to rotting the bunks or pitting the cylinder, you should consider that if water has penetrated the inside of the steel frame (which it probably already has) the water will expand when frozen thereby splitting the steel open and compromising the integrity of the steel structure.  You paid alot of $$$ for the lifts and therefore want to insure that they will be in service for many years to come.  Most dock companies that have a barge will be able to come by in the fall and lift the lift out of the water and place it in your yard.  Good luck with whatever you choose to do.