The title says it all. I'd like to make a time-lapse video in New York City, but most buildings do not allow tripods. Does anyone know where I can use one 'from above'?
This may be better suited for photography.SE
When it comes to private buildings access to using the observation deck or the roof is regulated by the building owner. Normally places with accessible observation decks forbid tripods without a special permit because they take too much space. There are blogs that make suggestions on what to do instead.
So the option you choose is up to you.
Ideally you'll want a place like Top of the Rock. However, they have a 'no tripod' policy, like Times Square and the Empire State Building.
HOWEVER, The Top of the Rock does allow you to take a tripod but without extending the legs - read this guy's experience doing this. So potentially you could try it and just extend them ever so slightly and get away with it.
How high do you need to be? Have you considered shooting from a higher street or bridge, such as the High Line, the bridge outside Grand Central Terminal, or one of the bridges like the Brooklyn Bridge?
Be sure to consider the security of your camera equipment when it's in one place for a long time, whether inside or outside a building. Don't take your eyes off it for a minute. This is one reason why the view from a hotel room may be a better option (but hard to arrange the exact floor and outlook, you might be at the back overlooking alleys!).
(update) However, setting up a full-size tripod on a sidewalk is only allowed if it's quite wide at that point (leaving at least 8 feet for pedestrians), and other rules, see NYC Filming rules (link from comment by @Karlson).