Let's clear up some inconsistencies in this thread.
First, the New York, Brooklyn and Rockaway Railroad (I think) originally ran down down to the waterfront in Canarsie for connection to a Rockaway ferry.
When the line was taken over by the BRT and electrified, it switched from third rail to trolley wire at Rockaway Parkway.
When the Broadway El became a subway line, so did the Canarsie line. The service to the waterfront became a shuttle.
Sometime in the 1920s, the Canarsie Landing service. became a trolley.
In 1942 it was abandoned, and replaced by a free transfer to the existing Rockaway Parkway trolley, which eventually became a trolley bus and finally a diesel bus.
In the 1970s there was a proposal which would have rerouted the Canarsie line onto the Bay Ridge line beginning at Wilson Avenue. Bushwick-Aberdeen would be abandoned, the old underground East New York LIRR station would be the new subway station for the L at B'way Junction, south of there it would run on the LIRR ROW instead of the El and would continue. The surface alignment to 105th and Rockaway Parkway would be abandoned. The line would then run crosstown to 62nd Street/New Utrecht Avenue.
As for the expressway mentioned, this was the Cross-Brooklyn Expressway, proposed by Robert Moses first in 1948. As of 1958 it was planned to be I-695 (why not I-295, it's not like it was going to run to NJ, the current I-NY295 was I-78). It would have started on the Gowanus at 65th Street (the Gowanus would be 12 lanes through Bay Ridge) and run along the Bay Ridge ROW to East New York, where it would connect to the Interboro, I-78 Bushwick Expressway and I-695 Queens-Interboro Expressway. In 1966 the city changed the plans, renumbering the road I-878 and rerouting it east straight to JFK Airport. At this time, the QIE was to have extended south to the Belt Parkway at Exit 14 and run along the Bay Ridge Row near Van Sinderen Avenue. The Canarsie el was to have been abandoned and replaced with median operation. The CBkE was canceled in 1971, the QIE a short time later.