A website that I've found useful is naval-history.net, more specifically this page, which gives the service histories of about 1,000 RN ships (including subsidiary navies like the RCN and forces of the governments in exile). This page also gives a day-by-day run-down of naval events over the course of the war. Combinedfleet.com is another useful one. This gives operational histories and tabular records of movements (TROM) for nearly the entire Imperial Japanese Navy.

Edit:

For the USN, you have the Dictionary of American Naval Fighting Ships, which gives brief histories of the ships of the USN, but doesn't go into the same detail as the other sites I linked.