If you are arriving in Hawaii at KOA, you would be better off laying over on the west coast since that would put you on a large # of flight options.
If you take the EWR-HNL direct you are then connecting in HNL to an interisland flight backward to KOA. Be sure to factor in any required interisland fares when you price out your flying costs.
Less backtracking and less interisland flights will be more time (and probably cost) effective....
East coast to West coast, to KOA, stop #1.
KOA to LIH (via connect in HNL)stop #2
LIH to HNL, stop #3
then back to the east coast.