There are 3 ways to get the professor out. The first is to try to negotiate with Captain Grim, need to talk to Razor and you'll be taken directly to the Captain. The second way is to fight your way to the professor. The main entrance of the pirate base is at G1, which can be reached if you go south of G3 or H3. If you're looking for a more stealthy approach, there is a hidden cave on the island at E4 that leads to a secret entrance to E3 but you need 11 perception to notice it.