On a seadoo boat, they have whats called a nuetral safety switch. Make sure the shifter is in the "N" position, then try to start the craft again. What leads me to believe its something else, is do to the fact, you mentioned that you got 3-beeps. I'm not sure what 3-beeps indicate, but 2-beeps, mean your landyard/mpem, are communicating with each other.
If you've drawn a conclusion, that, you do not have spark, then locate the igniting coil (spark plug wires attach to), and disconnect the white wire. Have in your possession a light tester, and while hitting the start button, testlight the white wire. No light equals, possibly a broken pickup sensor located inside the mag cover, OR, stator assy is bad.