Try the following:
Piedmont Airlines - they have bases in LGA, MDT and SYR - they are easy to commute to.
Colgan Air - Look at this link. They have a lot of bases in the NE:
http://www.colganair.com/bases.htm
Commutair - they have a base in BOS
Keep in mind, these are not all of the bases for these companies. I am not completely sure which is senior or junior...except for Piedmont. LGA, SYR, and MDT are the easiest domiciles to get right out of AQP. PM me if you are interested in Piedmont. I will help as much as I can - there may be some things that I cannot answer.
Lax