Item-by-Item Comparison of NJ Transit proposal and ours.
(Figures for NJ Transit proposal from Newark Star-Ledger 07-28-05, "Next stop 34th St., NJ Transit decides for its new tunnels", by Joe Malinconico.Estimates for Subway to Secaucus and comments courtesy of Joe Versaggi, Bridgewater, NJ)
Figures adjusted pro-rata from original total estimate of $6.0 billion to more recent NJT $7.2 billion estimate on 4-22-07.
NJ Transit proposal (Weehawken to 34th St.) Our Subway to Secaucus proposal
1. The new tunnels to 34th St. $2.7 $2.5 #7 Tunnels & Lincoln Harbor transfer station (85% of NJT's tunnels + $0.15 for station)
2. 34th St. station $1.9 No new NYC terminal
3. NJ track work - Boonton yard, Bergen Loop $1.6 $0.3 Elevated track from Palisades to Secaucus Transfer station + 10-track yard
4. NY track work $0.4 $0.1 NY track work, NJT share of junction at 10th Ave & lead into tunnel
5. Property acquisition, engineering, enviro permits, etc $0.4 $0.1 Less than for alternative proposal
6. New trains plus yet uninvented DMU (dual mode) 
elec-diesel locomotives (costs under-estimated by NJT)
$0.2 $0.3 11 IRT subway trains
7.  $0.1 Bus platforms, connecting escalators at Secaucus Transfer station
8.  $0.2 Contingencies
Total Estimated Cost (billions) $7.2 $3.6 Total Estimated Cost (billions)
9. Plus 2 extra tracks between Secaucus and Harrison and widening of N.E. Corridor Portal Bridge over Hackansack River to eliminate bottleneck, obtain full benefits of new tunnels $2.4
Revised Total Estimated Cost (billions)  $9.6
No figures available for Penn Station to Grand Central Station connection   $ ?

Item 1. The #7 cross-Hudson tunnels can be smaller, at steeper grade, hence less expensive than the NJT tunnels.
Item 9. Added in 05-24-06 revision of page.