regular ferry service from Orient Point, NY (tip of the North Fork) to New London, CT that is well worth investigating if you're intent on passing through New York City.
The ride west along the north shore of L.I. can be pretty nice in spots; a little more suburban/urban, obviously as you get closer to the city.
Please note, don't discount riding into the city on a Summer's weekday or a weekend. Like rvb1019 correctly noted, Summer Friday traffic heading OUT of the city can be a bit crazy, but so is the traffic headed OUT of the city in any direction on that day (my wife and I usually bolt on Fridays for the Catskill mountains to the North and the crawl up to the George Washington Bridge can be frustrating unless we actually leave work early and get a jump on it).
I live here currently. I've lived here all my life. When the commuters are home in their towns far away from Broadway, I'm right down the block (literally). Like we've all intoned, it can get a bit nutty, but that's to be expected: it's a BIG, big place. But if you're on a bike, you can literally park ANYWHERE (and believe me, as for crime, thieves barely notice Beemers and no you don't need a giant chain and lock) and frankly its an exciting place to visit. With the exception of Bubba and Snoone, most of the people I know who ride and ride in the city don't frequent this forum, so if you want some more insight from a larger group of NYC 2-wheel enthusiasts check out the Regional forum on Advrider:
And if you think you might be here on a Tuesday night, definitely stop by the EAR Inn in the Soho district of Manhattan. There's a big Tuesday meet that happens there every week:
Best of luck! Hope to run into you this Summer.