I am currently on my 4th year of H1B( H1B visa stamp till June 30,2014). My current hospital is filing H1B extension for my 3 year fellowship by the end of this month. I believe they will only give me two years of visa considering I will run out of my 6 years. Do you think this is the right time for me to apply for NIW or should I wait? In the rare case of petition getting rejected does it make future application more difficult?
Yes, you can apply under EB-2 NIW now. Once your I-140 has been approved, and if your country is still backlogged so you cannot file your I-485, your employer can extend your H-1B status in 3 year increments until you can file your I-485.
All I-140s are adjudicated individually. So, a denial of one I-140 should have no effect on a subsequently filed I-140.