Modern is fun, but heads up that you can't eat or drink in there. They do have a deal where they'll allow re-entry from the bar next door, though.
Personally, if I'm in Manhattan, Pioneers is the spot. If I'm in Brooklyn, I'll just start in Williamsburg — it's gotten saturated with amazing locations lately. Have you been to Sunshine before? If not, I'd go for sure.
Whenever I visit friends in NYC, somehow we always end up walking around all night shooting the shit. Wandering the city is the best. Hop in a bar for a drink, go grab a slice, head out somewhere else to see what's happening. Pinball Map makes this 100x more fun —pick an area to hang out in, and then consult the ol map to figure out what's next. If we get there and the scene sucks, no worries — there's usually something else five minutes away.