Build a tiny ship (one core should do the trick) and maneuver out in front of the ship that continues to move. Bang into it a couple of times from the front, to make sure it will stop. You might even consider entering the big ship with the tiny single-block ship. Once inside, you should be able to abandon the single-block ship and move about the cabin normally. I highly recommend aligning yourself with the ship. I think you can align yourself with the ship by simply pressing space while looking at a nearby block. You can also align yourself with the ship by activating an on-board gravity block if the ship has one.