24ft pontoon boat with 90 hp two stroke.

[steelespike]

The best speed for mileage should be around 6 to 8 mph.If you have the patience to go that speed.
There are speeds around there that it will sometimes out perform a runabout.
The best way to determine the best practical cruising speed is with a flow meter.
Some do real time calculation. Or you can simply note the best speed for a given gph (gallons per hour)

 

[lncoop]

You're really asking two questions. The first, what's a good cruising speed at what RPMs, is very subjective, but like you I find 14-15 mph at 3500 RPMs to be optimal for crusing. The second, what's a good cruising speed at what RPMs without hurting the motor, depends on the prescribed RPM range for your outboard. If you don't know what that is you need to find out, but I can say with 100% certainty that 3500 is well within it and will not hurt the motor.