I'm surprised nobody else mentioned it, but American Eagle has an LGA base. Pretty good outfit from what I hear, and the upgrade time is improving. Also XJT would be a good bet (in Newark), but that might be a bit of a drive. If you want EWR, you'll have a pretty good chance of getting it. AWAC is also opening an LGA base. I'll say this: Avoid having to commute at all costs. I would suggest avoiding Colgan as well.