it has to be open to all, or you have to be in the faction or on the crew list, then you just land or stand beside it and then hit the board button from the entrance of your ship. and then select the building and enter.
If you enter the skyscraper and it has a docking bay I could see it being in there. You enter it the same way. If your faction owns the skyscraper it should be able to grant you access. I hope this helps.
Edit: Skyscrapers do have docking bays and hanger bays so I am guessing the ship is inside of it. Contact the owner or if it is faction owned talk to them to see if you can get access.
Edited By: Pepi Deto on Year 14 Day 198 10:38 ____________
Commander Pepi Deto
Instructor, Ichigo Military Academy
Falleen Expeditionary Forces
Battlegroup 2 Executive Officer