The LG/LEVER disagree EICAS message is a warning, not a caution, and has the higher priority audio/visual(red) message generated.
The Embraer 145 QRH, which I have in front of me now, says that if such a message is received, the gear is to be cycled. If the message persists and the gear is to be selected down, then the abnormal landing gear extension procedure is to be used.
However, the drill does suggest in the preamble that that there would be a 'landing gear abnormal indication' indicated on the EICAS. There wasn't in this case.
Like many, I've always been told to trust what the gear indicator is showing - if you've got three greens, the gear is definitely down. It's changed my way of thinking for sure.
One last point, isn't it is surprising that at a busy airport like BOS that no other pilots noticed the a/c was coming in gear up and were able to say something directly or indirectly as a way of warning the crew.