Things to ask yourself:
Where am I working and it's relation to where I will live.
Parking? Do I want space to work on my car?
How much do I want to spend?
Some folks mentioned Brooklyn. I like Greenpoint, because there are still a few low cost rentals around. It's kind of like a mini soho.
The rest of the areas, good luck. I suggest you look in Queens as well. If you know where you will be working, then look around for something that will be a 20 minute subway ride. With rush hour, you should have a travel time of 40 minutes max.
I've lived in Manhattan as a kid as well as in college. I went to school in Manhattan. The "life" is way to expensive and not all it's cracked up to be.
Queens, Brooklyn and yes, the Bronx are great areas for first timers. The Throggs Neck section is still affordable, but clean and safe. Plus it is only a bus ride away from Manhattan.
Elmhurst, Forest Hills, Astoria, Middle Village are all in Queens and are great places to live. Though they are getting a little expensive. That's because these neighborhoods are all close to mass transit/highways/bridges/tunnels. Which makes getting around easy enough.
However, I found myself wanting more privacy as well as space. So I moved to LI and have more room and privacy for what a nice two bedroom goes for in Queens. Plus, I own it. Some may disagree and that's fine. Just think about what is important to you and how much you can afford.