Here are some.
http://home.comcast.net/~miketordoff/By_bike.htm
I don't think you need to go near Perth Amboy and I wouldn't.

For NYC to Newark, the best is the train, but anyone who rides in the area (including me if you can't find one) should be able to give route riding all the way from NYC over the George Washington Bridge. (Not worth it IMO.)

From Newark area to Labertville/New Hope, there are several cue sheets you can Google around for. Here are the simplest directions I found someplace (don't remember where - Major Taylor?) that looked like they would work.

Rt 27 South from Newark/Elizabeth area
into New Brunswick [can pick up D&O canal path in N.B. if you've the tires for it]
Rt. onto Franklin Ave.
Left onto Route 514 South
Route 514 south to Route 202 south
Route 202 south to route 179 south.

The first link I posted has much more elaborate ones. Or alternatively you can find cues to washington crossing area and then ride down the side of the river.

Here is the Phila bike maps, providing a number of choices to get from New Hope/Labertville into Philly, or anywhere else in the general area.
http://bicyclecoalition.org/map/map.html