Just a update on this I know now you can stealth to that location too before the professor is kidnapped if you don't have pick pocketing as a option. I had to blow up some rocks north east of Port Craig which let me enter the pirate base through a crawl space. I zoned west to docking area then entered the building to the north, Stole a key from the lockers which opens a door with 110 lock picking check on the top floor. In that same area with the key there is a pipe you can detect if your perception is high enough. The pipe take you up to the top floor right by the door, after that you're clear to loot the lower levels with out having to kill a single pirate. However the pipe you crawl up require a 8 agility to crawl back down, I was lucky I had some cave hopper leather armor and a cave hopper steak on me.
