Meeting people - straight or gay - in NYC, is like meeting people anywhere - if you're genuinely interested in them, they usually respond in kind, the city is just geography. The Piers on the West side highway on weekend days, in the West Village are teaming with all sorts of gay people hanging out and socializing; the East Village has some really - small and laid back gay Coffey Houses and bars that are very friendly.
Pick up a copy of Time Out and the Village Voice for alternative venues/ideas for meeting people. See if you can get an invite to the Soho House, from a friend or co-worker, who is a member, then hang out by the pool on the roof, or in the lounge (not a bar) on the 5th floor.
The Meat Packing district - always a good area to meet new people - as well as, union square and Washington Square - during the day. Just grab some food from a vendor and hang out on a bench or the grass for a while, not only will you meet people you should be quite entertained, as well.
If you want to avoid cliques don't hang out too much in Chelsea - Hell's Kitchen is fast going that way too.
Here a link that may be helpful
http://www.meetup.com/non-scene-gay-20-somethings-NYC/.
Don't forget the volunteer venues in NYC that you could explore.
Hope this helps.....