It’s not really a probability question, prr, because the NY Subway trains keep to a schedule (at least in theory!), so the best strategy ought to be deterministic (or at least any MTA screw-ups should on average affect each line by the same amount).
First, let’s look at the NYC Subway Map. For those not familiar with NYC geography, the OP’s point of origin at Forest Hills / 71Av is in Queens on the right-hand (eastern) side of the map, at the lower edge of the green area marked “Flushing Meadows Park”.
The E and F trains both run on the same tracks and make the same stops until the 5th Av (@51st St) in Manhattan. Up until this stop, there’s no advantage taking either train – just take the first one that comes. Between 5th Av and W 4th St (the OP’s transfer point), however, the F takes a more direct route than the E (6th Ave rather than 8th), which is why the “take the F then transfer to E strategy” might improve the OP’s chances if the F is the first train to come along at Forest Hills.
So much for map-based theory. Let’s look at some schedules: E and F (warning: both are PDF files). In general, during weekday commute times, each train is on a 4-6 minute headway, interleaved (i.e. one or the other will come along every 2-3 minutes).
From the schedules, the E takes 32 minutes to go from Forest Hills to W 4th, whereas the F takes 30 minutes. So, if the first train that comes along is an E, the OP should just take it all the way to the WTC stop. If the first train is an F, then one could take it to W 4th and dash upstairs, but why bother? The E that comes then will be the next E from Forest Hills, not the one previous to the F taken. In the best-case scenario (4 minute headways), the E and F will go through W 4th St at exactly the same time, leaving no time for the transfer via escalator.
The above analysis breaks down if there is some kind of unusual “differential delay” between the E and F trains, i.e. between the 5th Av and the W 4th St stops (presumably due to one of the ubiquitous “track fires” that I remember from my NY-subway-riding days). If this is known in advance, or announced at some time during the trip, the OP should take the non-flammatory route (E or F) between 5th Ave and W 4th, and proceed from there.
In other words, in general the OP won’t save any time by taking the F and transferring. The decision may boil down to a simple one such as: on which train is it easier to get a seat? [Here in the SF Bay Area, I’m convinced that there’s a PhD thesis waiting for the first person to crack the optimum BART-seat-getting-strategy for the various different lines, and the same is evidently true in other cities.]
Sorry the answer’s not more exciting, pseudotriton ruber ruber.