Quote (Sora-Chan)
Just cause they are going to that ship, doesnt mean that the portal gun will be on that ship, Aperture Science was probably working on more than just the portal gun, so theres most likely more than just that for tech.
According to Aperture Science's website (Yes, they had a mock-up website for it), the only other thing Aperture Science was working on was Military-grade Shower Curtains. Given how the big-mysterious-ship did-something-possibly-plot-vital, I'd say it's highly likely that the Portal Gun, or another version of it, is on board.