Edit: Knots are now in Sage!!!

Old answer:
As far as I know, there is not any knot theory in Sage, though there is lots of combinatorics and some algebraic topology.

The most natural thing to do would be to port the Knot atlas somehow, and (if one was very bold, and had permission) the Mathematica package that creates it. I have had people ask about this before, and it's a very natural thing to do in Sage. If you know the people in charge of this project, you should see whether they are open to this (if only for having two implementations of the same algorithm to check for bugs).

Update: Braid groups have now been in Sage for a while, including plotting.