Eelectrolosis doesn't attack the coating on your pontoons. It can attack the _meta_l where the coating is worn away.
When were talking electrolosis in most cases were talking stray current coorosion. You would be farther ahead to eleminate the sources of stray current damage.
Many Aluminum boats are not painted in fresh water.
Now lets talk about 5k for recoating your pontoons. In 03 I had the bottom on my 55 Pluckebaum sand blasted and 2 coats of Coal Tar epoxy applied for $2540 at Lee Spry Marine in Iuka Ms. They did an incredible job. You might want to shop around.
http://www.yandina.com/electrolysis.htmhttp://www.yandina.com/galvanicIsolator.htm