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Does the alarm system work on the engine? If yes, are you getting any alarm when the problem happens?
How old is the fuel, and when was the last time the engine made full power?
If the alarm is not going off then the engine is not entering safe mode.
Because of that, it sounds like the engine is probably starving for fuel. Have you tried pumping the primer bulb over and over with the boat at top speed to see if it makes a difference?
The next steps in troubleshooting this would be checking compression, checking spark output, and checking fuel pressure with the boat at top speed. Are you able to do these sets of checks?