EDIT 9/4/16 Apparently you don't have to clear every single building in each zone, you just need to complete each sub-quest and assign a raider gang to that part of the park. It appears siding with the Operators will net you the most caps and best loot out of the 3 factions.
After you meet back up with Gage after completing the last mission, he will task you with "The Grand Tour" aka clearing out Nuka World and staking a piece of the park for each Raider faction.
Simply clear out the areas of enemies where the way points tell you and then you will need to assign an Operators, Pack or Disciples banner to the flag pole in each section of the park. Each Raider faction will favor you more the more land you give them.
There are 3 sub quests in each area of the park: Kiddie Kingdom / Safari Zone / Dry Rock Gulch you will need to complete that are pretty easy and straightforward and started upon entering. For the Dry Rock Gulch section it is highly advised you have 7 CHR and 3 pieces of CHR gear (Formal Hat / Black Rimmed Glasses / Reginalds Suit is what I used) on you so you can choose the "Can we skip this?' option 3 times to speed up the quest and earn some easy XP.
You will also need to collect at least 20/35 star cores to repair the main frame for Star Control. Here is a guide of all Star Core locations https://www.vg247.com/2016/08/31/fallout-4-nuka-world-star-c...