I have run the boat several times this year with not problems. Safety switch is good. Turns over fine and seems to be getting fuel but no ignition.

Seems logical to replace the ignition coil and rotor button first.

Thoughts? Ideas?

Was it running this year or was this the first time you had it out for the season? 

It turns over (cranks with the key) but won't run on its own? 

Have you checked the safety lanyard? (gotta ask!)

With a carburetor you can remove the spark arrester and look down the carb as you open the throttle.  You should see the accelerator pump squirt fuel down the carb throat.   If that is dry you have lost fuel.

If it is dry pour a couple teaspoons of gasoline down the throat and turn the key, it should try to start or even briefly fire on the gas you gave it.   

If you still have nothing start checking why you have no spark.  Could be as easy as dirty points.

Start with the basics and usually the problem shows up.

So does this mean you checked to see if it has spark or just figure it's got no spark because it's not starting?

I'd verify that there's no spark with an in line spark tester or a timing light or holding a plug near a ground like the block while cranking the engine over.

A 99 351 (non gt40) has a carburetor and electronic ignition. The original was a Prestolite distributor with a Prestolite electronic module that's been out of production for a long time.

You have a multimeter? If you want to troubleshoot, you'll need one.to see if it's a wiring issue, a parts issue like the coil, cap, rotor or maybe  the electronic module itself.

Or you can replace stuff, starting with the cheap easy things and working your way up to a replacement module for the distributor 

So, more info would be a good thing  

Then unhook the supply to the the coil positive  and with the key in RUN. It should be about 12ish.

If that's good, then unhook the wires from the coil negative and remove the coil wire to the distributor so the coil has no wires attached and check the resistance between the positive and negative terminals on the coil. On yours it should be about 1.5 ohms.

Then check the secondary resistance between the positive coil terminal and the center terminal that the coil wire plugs into. it should be in the 8500 or so ohm range. (Make sure you're on a scale that lets you read to 8500)

If things are good hook everything back up and then hook the meter between the coil negative and ground (select volts on the meter) and while turning the key to start the engine watch the voltage on the meter.

If it's fluctuating between about 10 to 12 and zero, it means the module is doing it's job. It may not read 12 since the starter is drawing lots of current, but you should see a big fluctuation in voltage

If you have a steady reading of zero or 10 to 12, the distributor isn't working to ground  and unground the coil so it can make a spark.

If the cap and rotor and coil wire are in good shape, the likely culprit then becomes the electronic module.

Just work your way through the checks making sure you're reading the right thing on the meter (ohms or volts) and on the right scale for your expected readings.