If your ship is still docked in the settlement drive near the settlement then request docking permission in your SRV. This will allow you to drive to the landing pad where your ship is docked (a marker will show up on the compass at the top of the HUD) Drive into the bay almost all the way to the back then you can "Board" your ship.
The alternative is drive outside the fire restricted zone of the base and recall your ship. Your ship will fly to you and land nearby and you can board your ship once it has landed.
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