ok ........ shut off the Boston sub and play the speakers without using the sub. If you like the SQ, then its all fine! Would also suggest playing some bass heavy tracks on loud volume for at least 1 hour continuous. If the avr is on the weaker side, it MIGHT switch off on heavy bass numbers or the speakers could start squealing / clipping. The avr also might get very very hot. That would / could be an indication of it being under-powered, needing replacement with something more powerful.
Subwoofer performance is not avr related .... that has its own source of amplification.