The best is probably the new ship museum. They have a full size replica of a Dutch East Indiaman. Very impressive, although how they accommodated a crew of 350 is a mystery to me. Inside the museum the section on the 'Golden Age' has a good collection of ship models and other items. Not a lot on naval warfare but well worth a visit.
The Amsterdam Historical Museum has a collection of weapons and armour although sadly I missed their special exhibition on trade with the Ottoman's in the Levant. That will run until August.
The Rijksmuseum is of course the must do visit in any trip to Amsterdam. I have been a couple of times before many years ago and remember the wonderful dioramas in the basement that inspired me to start renaissance wargaming using Peter Laing figures. The museum is undergoing a major refurbishment so they have moved the Old Masters and other selected exhibits to a single wing. Still worth the effort and here there was an Ottoman exhibition with a number of books and plates.
This one of the siege of Vienna was especially interesting.
There are a number of paintings and exhibits of naval warfare and the Dutch colonies. Plus one of my favourite pictures - Rembrandt's 'The Night Watch'.
Amsterdam is a lovely city, and even without much of military interest, still worth a visit.