There is absolutely no reason to check in 3 hours early for any airline in the US. AFAIK, all carriers servicing the US insert that language based on DOT recommendations, which aren't for experienced flyers.
Air Berlin actually publishes their check in cut off times at different airports. Some in the US are 60 minutes, others are 90 minutes. At BOS, it is 60 minutes.
https://www.airberlin.com/en/site/checkin.php