The time is the departure time from the ferry terminal in either New York or New Jersey. I don't think you need 90 minutes for security - when I went, we were told to be at the departure point at least half an hour before departure to clear security.
In my opinion, visiting the Statue of Liberty is not worth the time it takes. The crowds are simply horrendous and you'll spend most of your time queuing - for the ferry, for the statue and, particularly, for the ferry to leave Liberty Island again. (If you get off at Ellis Island on the way back then you'll also have to queue to re-board the ferry there, too). You should count on at least four hours, and probably more.
Similarly, the climb to the Crown is hot and hard work. You stand in line for ages, then it's a tough 15-minute climb for the chance to look through a tiny window before spending 15 minutes coming back down again.
I love New York, but there are much better ways to spend your time than going to Liberty Island. Just take a ferry to Staten Island, which gives you a decent view of the statue and the Manhattan skyline for nothing.
But if you're determined to go then snap up those Crown tickets now, as they're normally sold out months in advance.