As another data point, you can find some great deals with a 30ish minute commute in Brooklyn. Yes you can easily pay as much as UWS/Tribeca but there are more deals out here.
Another pro tip: ride a bike and save $5/day on your commute!
If you want the ultimate in NYC luxury, find an apartment within walking distance of your job ... you can pretend that the $100 / month you save on a Metrocard makes up for the rent increase. A 5-10 minute walk-to-work commute is probably the single greatest quality of life improvement money can buy.
Brooklyn is a great idea. Also "Long Island City" in Queens. Hoboken, Jersey City. If you live near the subway in those places you can have a 20 min ride to midtown/downtown NYC.
I lived in Hoboken for three years while working in NYC. First, I'd recommend living very close to the PATH station. The buses are very hit or miss, depend on traffic, and don't run frequently on weekends.
Also, if you're out in NYC on a weekend and want a cab home to somewhere like brooklyn, it'll only cost you like 15 bucks. However, if you want one to Hoboken, it'll cost you around 50-60... Really a pain when the PATH only comes every half hour after midnight.
Hoboken's where I live and I love it. Rent about 50% of what it'd be in the West Village, just across the river. PATH train makes for a quick commute and runs 24 hours. City is walkable, Fresh Direct delivers, Grimaldi's and Maxwell's are here...
As long as you can walk to the PATH, the loser factor on weekends (Jersey's finest comes to party) is the only real downside.
Another pro tip: ride a bike and save $5/day on your commute!