Depends on your cost/time tradeoff.
Manhattan is extremely walkable. If you live close to where your office is, you might be spending 10 minutes commuting each way (including elevators in both buildings). That's rather short, but not unheard of in NYC. However, it might be more expensive.
If you (say) work in Chelsea and live in deep Brooklyn, you'll have 40 minutes commute each direction each day, and that would save you some $1000/month on rent. Some people would rather pay that money than spend that time daily.
Jersey City and hoboken are, in many senses, close than Brooklyn or Queens, definitely closer than Long Island City. The commute is not bad at all, as long as you find a place close to a PATH station, and your office is walkable from a PATH station (if you need to switch between the PATH and the subway, you'll have a much longer and more expensive commute).
Don't immediately discard manhattan - there are good deals to be found, and brooklyn is not as cheap as it was five years ago.
Finally, if that's feasible, I'd recommend finding a one month rental (airbnb / sublets on craigslist, corporate housing / long stay hotel if you can afford it) close to your office BEFORE you commit; that would let you get a better idea of what you need and what's your cost/benefit tradeoff. Basically all reasonably priced nice apartments in NYC are yearly contracts, and many owners will not let you out easily if you want to leave earlier than that.