If you choose Skywest, you'll get LGA which is an ERJ175 base. Upgrade on the 175 here is something around a few years I think. You'll probably upgrade sooner at PSA, if that's a priority for you.
Otherwise, pay is similar post contracts. SkyWest has a lot of open time to pick up. My experience with the company in my 10 months here has been mostly good.
4 year degree? If not, the flow is nice to have even if it does take 7-10 years right now. I also hear the SAP thing is pretty cool.
In the end, their both regionals. Pick the one that will cause your life to suck the least. IE pick the better commute, and one that will get you out of there faster.
Btw I moved from Pittsburgh to Denver n@