Hmmm, "the best" is always a tricky question. Inside Media 100 you have some choice of Chromakeyers, either the internal one or the ones built into Boris Red. They work pretty well for some footage.
You also can use Ultimatte or Primatte inside AE, or Keylight which is pretty good and included in AE for free. Personally I think Ultimatte is one of the best keyers for challenging material, but usually not too fast, and as far as I know they haven´t released a version for AE CS5.5
I've always used Keylight in AfterEffects and the results were very good. However, as an experiment I tried the new keyer in Motion 5, and found it to be much improved over Motion 4. The reason I mention it is that Motion 5 is just $49. So for chromakey work, I don't think you'd have to pay the $$ for AE when you have options with Boris and, as of now, with Motion 5.
I think Boris Red 5 Chroma Key set-up is ok. And may be all I'll need for the future. I was just wondering what other M100 people were mostly using. In the late 90's I had a plug in for M100 from Ultimatte that worked nice. For the last few years I've been farming out my AE work so I really know little about Keylight.
With more Chroma Key work coming in the future, I need to bring the work back in-house. I would invest in AE and learn Keylight if it were the best way to go.