I am a firm believer that there is no "best sytem" and that it can even vary from user to user.
This is based on the following thoughts and observations
1) a friend and I compared my 100-400 on Sony A700 with in body vs. his Canon 40D and 100-400 with in-lens. We compared 40 handheld shots at 1/125 and 40 at 1/25 sec at 400 mm. Number of sharps shots was equal between us. Then we switched, he used my camera and I his. Again similar number of sharp shots between us, but much less (just over half) of what we had using our own system. He was put off by not having the stabilisation visible in the viewfinder, while I was distracted by it and was continuously looking for the (non existent) shake bars. Typical case where familiarity and personal preference determine the winner, not the actual hardware.
2) In body will stabilise any lens, not many systems available with stabilized primes from 20 - 600 mm, but some IS lenses (if you have them) will likely perform better. So what do you want, the best for a few lenses or less performance for all your lenses. Again, no right answer, it purely depends what you want and need.
3) In my mind high iso noise performance after careful exposure and optimum PP to remove noise/keep detail is hardly different between systems of the same technology vintage. Pixel peeping yes there is a difference, in practical use I think it's insignificant.
So before we can answer your question you need to tell us which bodies/lenses you're thinking about and then "maybe" some people could give some pointers which would perform better under certain circumstances.