They're essentially the same. Ponder means to explore it in your mind. You would normally say you were contemplating something if you were thinking about doing something or thinking very deeply about something. (Ex: "I was contemplating life" or "I was contemplating going to Japan, but I decided against it.") To meditate on something means that you take time aside to really think deeply on it. So it has the same meaning but you would only use if it were something very serious that you needed to meditate on/think about. It often refers to something that happened, and you need to take time to reflect on what happened.

To expand on Cameron's excellent answer, meditate can also be a specific set of techniques that are taught (i.e. meditation).