I think this is what you're looking for:
Go to component mode (F8), then look at the masking modes in the status bar. Turn them all off, then right click the question mark and turn on local orientation. You'll see the pivot points in the joints, which you can rotate as appropriate. I don't know if those are the real names of things, I'm just guessing as well as I can remember (don't have maya here). Hope that helps.