After you talk to Elisabet, walk up the stairs to her left and look for a sign that says "Crow's Nest" with an arrow to the left.
Climb up and up and UP the ropes as far as you can go -- and this is the crow's nest. Thank goodness this is a computer game; in real life I would have had to stop halfway up to throw up.
There's nothing to do here except look around, until you read the journal in the desk in the captain's quarters.
Oh, and take those pieces of paper with flowers on them. You'll be gathering those for a puzzle in Magnus's cabin.