The in-progress East Side Access (ESA) project linking the LIRR to Grand Central is scheduled to open in 2016, and Metro-North is already studying options to use space vacated by the LIRR to run its own trains to Penn Station along the Northeast Corridor. Thus the basic service pattern will look as in this map. Observe that alongside Sunnyside Yards, there’s a stretch of track between the split between the Northeast Corridor and the LIRR Main Line, and the split between the access tracks to Penn Station and the ESA tunnels.
This should be turned into a new junction station, Sunnyside Junction. At this junction, passengers could transfer cross-platform between trains to Grand Central and trains to Penn Station, just as they do at Jamaica between trains to Penn Station and trains to Brooklyn today. If Metro-North diverts half of its 20 peak New Haven Line trains per hour to Penn Station, and the LIRR diverts two thirds of its 36 peak tph from Penn Station to ESA, then the service to each Manhattan terminal will be about equal.
Since both Manhattan destinations are of high importance, no train should skip Sunnyside Junction, not even peak-of-peak LIRR express trains that skip Jamaica. (Trains should not skip Jamaica, either, but that’s another matter.) Thus off-peak frequency could be assured to be fairly high, comparable to that to Jamaica (about a train every 10 minutes), and peak frequency would be so high that the transfer penalty would be negligible.
An advantage of this setup is that even at the peak, one-seat rides to each destination would become unnecessary. Therefore the interlockings and switching moves could be simpler, and new grade separations should not be necessary. In the off-peak, the transfers should be timed, even across agencies; this should be the first step of good regional rail service. Note that I advocated something similar as part of a comprehensive regional rail plan for New York, but Sunnyside Junction could be built independently of it. Indeed the interlining that minimizes switching moves and conflicts is not the same as the through-running in my original plan, which is based on matching ridership at the New Jersey end to ridership at the Long Island or Connecticut end.
Because a stretch of straight track for this station already exists, all that is necessary is platforms. Because all trains should stop at this station, and the capacity limit lies elsewhere in the system (namely, in the ESA tunnels), it would suffice to have two island platforms and four tracks serving them, and two additional bypass tracks to allow Amtrak to skip the station even at peak hour. If the station became very busy then two additional stopping tracks could be required, and construction should leave space for them.
To ensure the station is well-patronized by transferring passengers, like Jamaica and unlike Secaucus, it should not feature fare barriers or other obstacles between the platforms. Transferring should involve walking a few meters from one track to another, on the same platform. This is perfectly compatible with the current regime of requiring conductors to check every ticket on the train, because Penn Station and Grand Central are both in the CBD and thus the fare to them should be the same. The rationale for the faregates at Secaucus is that fares to Hoboken and Penn Station are different, and conductors would not have time to check that everyone on a train from Secaucus to Penn has a valid ticket to Manhattan; this is irrelevant to Sunnyside.
In the future, the LIRR and Metro-North should consider lowering in-city fare and raising frequency, which could work with more modern operating rules (i.e. proof-of-payment instead of conductors checking all tickets). Seamless fare integration with the subway would open the door to direct Queens-Bronx service; Metro-North is already considering Bronx stops for its Penn Station service. It would also give Queens another access point to Manhattan, slightly decongesting the near-capacity Queens Boulevard subway; the reason I say slightly is that the worst problems are far east of Sunnyside. And frequent service to the rest of Queens and to Manhattan would provide another public transit option to the area.
Unfortunately, the LIRR seems to not make any plans for such a station. It had plans for a station west of the split, serving only Penn Station: see page 13 here. I do not know if such plans will ever materialize in light of ESA’s cost overruns; I cannot find a more recent official reference to them. A cross-platform connection seems to never have been on any official agenda. Fortunately, even now it should be possible to add one, at relatively low cost since this station would be entirely above ground, and with minimal disruption to service since the site is a wide railyard with 6-8 active through tracks.