I use Sigil to set the line-height in the stylesheet, usually on the p tag, e.g.,
If there is already a p tag in the stylesheet then you need to add it to that. You can also be more selective--perhaps you do not want to set the line-height for all paragraphs, but only for some styles?
Also, some epubs do not use p tags for paragraphs, they may use divs or spans. This is annoying, but with Sigil you can easily check for this.