You can change the distance between chromosomes as well as the height of the ideogram or the data panels using the "plot.params" argument in plotKaryotype.
In your case you'll probably want to increase the value of data1outmargin but there are many different parameters to adjust. You can see them all calling plotDefaultPlotParams and giving it the plot type you are using. For example, for plot type 2 you would get something like this.
This function can even receive a plot.params object and it will adjust itself to plot the given parameters to help you understand the plotting process. I've used that many times.