Yes...all three shuttle cities have check-in counters in the gate areas. Also if your inbound flight is late, they will protect you on the next flight...they run hourly. Finally if your flight arrives early you may be able to get on the next flight...i.e. you take the 8A, and arrive at 850A, you might just get on the 9AM back. Before the shuttle flew BOS>DCA I used to "double shuttle" and would go BOS>LGA>DCA, and often could get right on the next flight leaving in say 5 or 10 minutes. Traffic is especially light on weekends, etc. For those interested, right now, they have shuttle go fares. I.e. BOS>LGA is about $89, etc. For coach seats, the shuttle has more room, and you can get free beer and wine.
Also during the week, they have meals during breakfast/lunch/dinner times....delli meals for lunch/dinner. During the week they also have Fox News Now on the audio system. Finally, the shuttle has discontinued offering the Sam Adams bottled beer.