In the comments to my last post on Queens Boulevard trolleys, Alon Levy offered a compelling argument that it would be impractical to connect the Flushing Line to the 60th or 63rd Street tunnels (or both) and thus free up the Steinway Tunnel for the purpose it was originally built for: trolleys. He may very well be right.
We can still put trolleys on Queens Boulevard, though, and still run them to Manhattan. Remember that the old Queens Boulevard trolleys used to go to Manhattan across the Queensborough Bridge. The right-of-way is still there, and so is the underground trolley terminal.
This could even be used for a Bus Rapid Transit "Quickway," but steps would have to be taken to make sure that the terminal doesn't get filled with exhaust fumes. For example, hybrid buses that could drive through and idle without running their generators, or enough clearance for natural gas buses.
Of course, the terminal no longer connects to the Second Avenue El, but as I discuss in the "Bridge xRT" post linked above, it can connect to the planned Second Avenue Select Bus, especially if an exit is built on the west side of the avenue. It could even connect with the Second Avenue Subway if the planners had given that some thought.
Also, the right-of-way is there, but occupied: the "South Outer Roadway" is used by cars and the North one is used by bicycles, pedestrians, construction vehicles and cop cars. There used to be a passenger deck on the outside of the upper level, as can be seen in some of the photos on Joseph Brennan's page. It might be possible to reconstruct it, but it would probably not be possible to make it wide enough to accommodate the existing bicycle and pedestrian traffic, which is often in conflict on the North Outer Roadway. Because of this, two lanes of the upper deck should be allocated to bicycles and pedestrians.
Again, I know, an expensive and politically difficult proposition. But it would bring several benefits. First, and most important, it would calm Queens Boulevard. Second, it would bring rapid transit to the underserved area between 49th Street and Grand Avenue - hopefully getting people to switch from cars. Third, it would capture local traffic along the Boulevard and reduce crowding on the subway and el lines.