Thank you your suggestions. For the return trip, we will stay on MetroNorth all the way to GC, as our final destination is midtown Manhattan. It's only on the outbound that we need to connect from Amtrak to MetroNorth because we originate in Newark and terminate in Greenwich, and this seems to be an easier connection than taking NJ Transit to Penn, taking two different subways to GC, and then a MetroNorth train to Greenwich.
Separately, I've noticed that Amtrak is frequently late between NY Penn and Stamford, particularly the Acela trains. 15-30 minute delays are not uncommon. Does anyone know why? They can't really blame freight train interference on that segment. Unless MetroNorth prioritizes its own trains over Amtrak, which would be a shame.
If you are northbound, your Amtrak will have no MetroNorth delays between Penn Station and New Rochelle since there is no MetroNorth service on that portion of the route (yet).