Better in what context?
As a goal scorer and a #9, Harry Kane is superior and he is also superior aerially. He is a much better and consistent goal scorer than Wayne Rooney has ever been in his career. Then again, you could argue that Harry Kane never had to adapt to another main striker and you could argue that teams are much better at constructing attacks in this era than when Wayne Rooney played due to the vastly superior coaching. Rooney was unfortunately (well fortunately for Manchester United) the water boy for Cristiano Ronaldo when Rooney was in his physical prime.
In terms of work rate, They are about the same.
In terms of ball control, Wayne Rooney was better when he was younger and he was a superior ball carrier. Harry Kane's ball control, especially his ability to resist pressure has improved vastly though.
In terms of passing, I would give it to Harry Kane.
Versatility, Wayne Rooney wins as he could play multiple positions on the forward line and he was faster.
It would depend on the team you are building. If you want a more versatile front line like Manchester United had from 2007 to 2009, then I would pick Wayne Rooney.
If you wanted a main goal scorer, I would pick Harry Kane.