I also had this problem -- getting back to the Valkyrie. I must have been driving the speedboat behind a battleship and the Valkyrie carrier for maybe about 45 minutes. Finally I gave up.
A plane did fly over. I have been playing this game on the Xbox 360. At one point I was able to drive up alongside of the ship, either side, but there is no way to re-connect with the Valkyrie ship. I will try to start over as others have suggested.
