First off, NYCT did not run surpluses. It ran lower deficits than it had anticipated running, but they were NOT surpluses.
Second, riding on the express buses exploded largely because of the fare reduction from $4 to $3 (with MetroCard users paying even less).
Third, most NYCT express routes don't go through New Jersey (remember, not all NYCT express routes operate between Staten Island and Manhattan), yet ridership increased throughout the express system.
No NYCDOT routes go through New Jersey (since none are Staten Island routes, that makes a great deal of sense).