I, personally, wouldn't suggest running as good way to build fitness for waterskiing.  Running puts a lot of stress on the knees which are quite important to a water-skier.  If you do want to run, make sure that you have the proper training shoes to minimise the stress on your knees, or use a running machine  these have more give in them, and will reduce the strain.

So what is good  cycling, stepper and climbing machines, cross trainers, rowing, and even walking.  The best thing is that all of these will help to build strength as well as improving your general fitness. 

OK, so you now have a good level of aerobic fitness, so what is anaerobic activity?  This is where you put your body, heart and lungs through shorter periods of intense strain then rest for a period before repeating the strain.  This is what happens when you slalom ski.  A good way of working on this is using the same machines as for the aerobic exercises, but rather than staying at the same pace for 15-20 minutes, increase the effort and speed of your workout for about 30 seconds, then reduce the pace for a further 1 minute.  Repeat this for about 10 minutes.

[AEROBIC FITNESS]   [LEGS]   [MIDRIFF]   [UPPER BODY]   [ARMS]     

For a full training guide including day by day waterski fitness program take a look at the
Complete Guide to Water Skiing.  The book also includes advice on diet and loads of
on-the-water training tips and drills.