Make sure they have check marks next to their names, and command them to board entity, your ship.
Or go old school and add them to join you, and manually board the ship then disband your group.
Daenarrah, there are two ways to perform that action. Both can be found via the Party section under Control at the right hand menu.
The first method is the easiest, however, it can take a while depending on how many NPCs you want to move. Of course make sure you have room (enough passenger count) in the ship you want to move them. Also be cautious not to fill up the passenger count lest you be unable to board the entity yourself. After you click party you'll see the option "Add to Party" next to any droid or NPC you own or are assigned Supervisor or Manager. Simply add the NPCs to your party, move your character aboard the ship and then use the "Kick from Party" to leave them on the ship. If you don't kick them then the NPCs will continue to move with your character wherever you go provided there is room.
The second method is like the first but rather than adding them to your party you can click each box next to all the NPCs you want to move. Clicking the large bold header of "NPCs" or "Droids" will select all those you are able to party with. Then scroll to the bottom, there is a drop down menu. Select from the menu "Command: Board Entity." You'll then be presented with all the entities you have access to, simply select the one you want and complete the action. All the NPCs and/or droids you selected will then board that entity. This is useful when moving large numbers of either. Once again, be sure there is enough passenger room for all the NPCs you want and at least one extra space for a player to move aboard.