IMHO, MOVE!! 3 hours a day on a commute is rough! I know DH used to drive 3 hrs to pick up SD every Friday &Sunday. When I was able to go with him, I was amazed how exhausted I felt after the trip! I can't imagine doing it daily! When you add in the extra care a 10 week old requires (Congrats by the way!!), 3 hours is a long time! I think a little boy would benefit more by spending time with his dad than going to the same school with kids he's known since Aug. This is kindergarten, not Senior year in high school! Also factor in that kids were out of school for a few weeks already for Christmas break, so your LO is already sort of used to not seeing them. Make sure you get contact info if there's a special friend LO wants to stay in contact with.
I agree with PP about seeing if LO could remain in school #2 until the start of the 2013 - 2014 school year would be easier than transferring to school #3.