If a player is the highest run scorer and at the same time is the highest wicket taker in IPL, which colour cap would he wear?
I see two questions here:
What caps would he be given if he's both the highest wicket taker and the leading run scorer?
According to the rules, both the caps would be awarded to the player, after the respective innings in which he earned them.
What cap would/should he wear if he's awarded both?
There isn't any rule which binds the player to the colour of the cap which he should be wearing. It is a personal choice for the player. (which is already addressed rightly in the comments under the question.)