from what i heard, the LIRR Port Washington Branch (IIRC) will be used as the transit link for the athletes at the village. it will extend from the meadowlands to somewhere past the shea stadium stop.
Water shuttles all over the place, extra service on some lines, and the 7 extention are the only solid bits of information I have heard. Don't be surprised if specials expresses were implimented on the LIRR or MetroNorth or in the subways.