While I am a huge Google fanboi, the biggest downside that I see to using Google Wave is that its not just in an 'eternal' beta phase, its very young technology. Google is still tweaking the API. Couple that with the fact that Google is still pretty new to the corporate applications arena and you're setting yourself up for likely disappointments and failures early on. Given a couple of years, this will probably be a superior solution but I for one am not convinced that its ready for prime time.
On the other hand, Sharepoint is a much older, more established application with a proven track record and a solid code base. Of course this fact tends to be a double-edged sword because that means that it also suffers from design decisions and coding practices that could now be called archaic.
I suppose a large question for you then is whether stability and reliability are more important in your choice of collaboration tool, or if you'd rather go with a tool that is likely to pioneer the next generation of online collaboration and suffer the bumps that will surely accompany your journey.