...is in the Prudential center garage. They have a dedicated bike parking section on P2 that's right in front of the security office. The monthly tag holders park there as well, so it tends to get crowded late at night or before bad weather, but there should still be space available, either behind the concrete/metal U-bars and in the narrow yellow lined spots by the car rental service or in front of the row of bikes. Just make sure to grab a ticket at the booth at the regular entrance off Huntington Ave. and stick it to your bike, or they might (read will) tag you for not being a monthly pass holder.
http://www.prudentialcenter.com/gettinghere/index.php (rates are for cars, iirc).
HTH,
Matt