If you own the NPC's you could fire one of them to remove them. In some circumstances we did have a kick passenger button which will transfer a passenger to the entity you are in, ie if you are on a vehicle onboard a ship.
Do make sure however that it isnt just because you have too many people in your party and that isn't what is stopping you boarding. So can you board your ship solo?
Okay I think I've fixed it, what I did since I had two ships one sprint (where the NPCs where) and a YT-1300, I got in to my YT and unloaded my passengers and started kicking people out of the sprint in to mine and then out on the planet it took a little while but I finally got in.
Odds are for people who want to minimize there own risk, SO NEVER TELL ME THE ODDS!!!