There is at least a perception of increased and/or unpredictable security lines post 9/11, even if the stated minimum of 20 min survived.

More broadly, other possible factors include increase in traffic delays getting to/from airport (def applies mid-town to LGA) and speed, reliability and comfort improvements on Acela. The train has definitely eaten more into the LGA-DCA route, but BOS has certainly been affected too.

I suspect that costs of operating the shuttles have grown faster than average fares as well, reducing incentives to invest in a robust/differentiated product and schedule.