The answer about Thread.sleep() being unreliable is correct: you can't count on it to return in exactly the amount of time you specify. In fact, I'm rather surprised your metronome is usable at all, especially when your system is under load. Read the docs for Thread.sleep() for more details. Max Beikirch's answer about MIDI is a good suggestion: MIDI handles timing very well.
But you ask how to do this with audio. The trick is to open an audio stream and fill it with silence between the metronome clicks and insert the metronome clicks where you want. When you do that, your soundcard plays back the samples (whether they contain a click or silence) at a constant rate. The key here is to keep the audio stream open and never close it. The clock, then, is the audio hardware, not your system clock -- a subtle but important distinction.
So, let's say you are generating 16 bit mono samples at 44100 Hz. Here is a function that will create a click sound at the requested rate. Keep in mind that this click sound is bad for speakers (and your ears) so if you actually use it, play it at a low volume. (Also, this code is untested -- it's just to demonstrate the concept)
int interval = 44100; // 1 beat per second, by default
int count = 0;
void setBPM( float bpm ) {
interval = ( bpm / 60 ) * 44100 ;
}
void generateMetronomeSamples( short[] s ) {
for( int i=0; i<s.length; ++i ) {
s = 0;
++count;
if( count == 0 ) {
s = Short.MAX_VALUE;
}
if( count == interval ) {
count = 0;
}
}
}
Once you set the tempo with setBPM, you can play back the samples generated by calling the the generateMetronomeSamples() function repeatedly, and streaming that output to your speakers using JavaSound. (see JSResources.org for a good tutorial)
Once you have that working, you could replace the harsh click with a sound you get from a WAV or AIFF or a short tone or whatever.