I've been waiting a long time for this, NJ TRANSIT Rail is now on Google Transit!
The route on this map is a sample trip from the Cooper St Rutgers Station (near the Ben Franklin Bridge) to the north section of the Henry Hudson Bikeway along the bayshore in Matawan.
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As you also may be aware there is a campaign to encourage Google to establish a bicycle trip planner. Over 23,000 signatures to date. Google has not commented on the subject, but they haven't said NO, hmmm. One major problem is that there is no standard for bicycle mapping. Different governments have different ways to rate roads. Half the battle is trying to establish uniform criteria.