The first thing to know upon entering the Lighthouse is that all but one of the undead wandering around aren't hostile, so don't attack them.
There are two buildings to either side when you first enter, and the lighthouse right in front. The two side buildings are storage for undead.
Upon entering the Lighthouse itself, the room to the east is a bedroom. The chests and dresser are trapped in a way that cannot be disarmed.
The room to the west is the library. You'll find Nekaros here, who's the lighthouse keeper and also a necromancer.
If you go to the end of the hall in the northwest and check the western wall you'll find yourself in a secret room. There's a horrid spectre in here. Talk to him and then he'll attack you. Once you've killed him you can pick up the Spirt Call Mind Crystal. Don't use it however. You need it for a future quest.
That's all there is in the Northpoint Lighthouse, so next we'll head to Hectar.