Much is made about about how far up from the ocean the Port of Philadelphia is, however, the channel is 102 miles long; at a leisurely 10 knots, that's 10 hours to the port, vs the 4 hours it would take to get to NY from that point. However, the Ports of NY/NJ suffer from major congestion and delays. When it is all said and done, the delay visiting Philadelphia and getting back down the channel is offset by the congestion ships face trying to berth in NY, to say nothing of the problems faced getting merchandise and goods out of the area once offloaded from the ships. The entire delay could last several days, versus roughly the day and a half it would take to get a container up the channel, off load it and send it on its way, and get the ship back to the ocean. A couple of shipping lines mentioned the congestion as a factor in why they transferred their operations from Newark to Philadelphia, namely Sea Star Line and Horizon Line.
As for the draft problems, last year the MSC Judith became the largest vessel to ever visit the Port of Philadelphia. Her max draft is 47ft, carrying a little over 8,000 TEU. While she did not come into the port fully loaded m, once the channel is finished being dredged she could at high tide, and unlike the Ports of NY/NJ, the main container port(s, once South Port is finished) is not encumbered by height restrictions; the lowest air draft over the Delaware Channel is under the Delaware Memoral Bridges at 190ft, which could accommodate all but a couple classes of the ery largest ships. All but one of the Ports of NY/NJ must deal with the 151 ft air draft under the Bayonne Bridge, and that one port still suffers from the severe congestion and associated delays.
Philly isn't trying to become as big as, say, the Port of Newark. Should they capture just ten percent of traffic currently going to Newark, let alone all the Port of NY/NJ, it would more than double what currently moves through the port, and the major hindrance to all of this, according to the shipping lines, is the 40ft depth; 45 ft allows them to expand their operations. (That's another thing: the major lines aren't talking about establishing new services, just expanding on the services they already have going to the port).
Concerning railroad options, besides CSX Greenwich Yard, Philly actually is served by two NS terminals. The more well-known one would be Morrisville Yard, northeast of the city. However, NS also has Mustin Intermodal Terminal, adjacent to Greenwich Yard at the port. It was established on the former location of the Mustin Air Field, which served the Philadelphia Naval Yard. A labor dispute let the yard idle for a long time, but it has begun to see some service; I saw pictures of a stack train being unloaded there from a year ago.