The issue is more than just the raw signal level 99.5 delivers in the Back Bay. It's the overall signal level on the FM band in the neighborhood, which is off the charts because of all the FM signals (92.9, 96.9, 100.7, 104.1, 105.7, 106.7, 107.9) transmitting from the Pru just a few blocks away. This causes a phenomenon called "desense" - there's so much RF hitting your radio in the Back Bay that it becomes unable to pull even a fairly strong signal out from under the much, much stronger signals emanating from the Pru.
This is not at all unique to the Pru and the Back Bay. If you live in the parts oif Newton and Needham near the tower farm, radios there overload from those FM signals (90.9, 94.5, 98.5, 102.5, 103.3) in a similar way. And believe it or not, even 99.5 itself can have a similar effect on radios in close proximity to its transmitter site in Andover. (I experience something similar here in Rochester, where I'm less than a mile from a site with six FM transmitters - anything in town broadcasting from any other location may as well not exist here on cheap radios.)
There's no easy answer to this. As others have suggested, the WCRB programming is also available on the W242AA translator at 96.3, broadcasting from the same MIT location as WMBR 88.1, as well as on WGBH's 89.7-HD2 and via streaming audio.