I had this issue on my Mastercraft X-14 the solution was to install a relay between the radio and the battery. I put in a house battery but this didn't solve the issue. The problem is caused by a voltage difference from the alternator, battery and to the radio head unit. I tried all the other options above and nothing helped. The relay completely solved my issue.
Below are the steps I followed for my boat from an expert on the mastercraft forum. I'm not an electrical whiz but doing this solved my issue. Don't ask me questions about this as I can't answer.... I just followed these steps to a T and it worked :)
This is the Relay I used.
Steps I got and followed - credit goes to JimN from Mastercraft forum
Use distribution blocks for the main + and - cables at the amplifier- it prevents the need to jam wires in where they don't fit. You'll need a Bosch relay for this- get one with a diode for suppressing voltage spikes.
Step 1- Feed a Red and a Black wire (12ga) from the distribution blocks to the head unit.
Step 2- completely disconnect the head unit from the boat harness and cap the yellow wire.
Step 3- connect the red wire from the boat harness to tab 85 on the relay and connect the black wire to tab 86.
Step 4- connect the new red wire to the yellow wire and to tab 30 on the relay.
Step 5- connect the head unit's red wire to tab 87 on the relay.
Step 6- Use a ring terminal to connect the black wire from the head unit and the new black wire from the grounding distribution block, then use the screw on the back of the head unit to secure them to the head unit.
Use a wire tie to secure the relay to the harness and the proper terminals on the wire ends. It's best to use a fuse at the end near the distribution block for the new red wire.
This tends to be the best wiring scheme- the amp(s) and head unit are connected to power at the same point, so there's no reason for whine to occur but it's still possible. One reason it's best to do it this way- if the resistance between the head unit and amp(s) is high enough, damage can occur, somewhere (depends on which circuit is most sensitive to it).
Tap 30 is the Hot and the yellow wire provides memory for the radio, as well as main power- the red has become more of a 'switch-enable' connection that turns on when the key is turned or an accessory switch is used.