I live in San Diego for 6 years and frequently flew SAN-BOS in search of flat beds. As far as I know your only domestic flat bed option into was a daily DL 767 from ATL and the B6 direct. I am looking at the summer schedule and I don't see it there. I do see a few 753's (75Y a/c) and they have a non lie-flat "Domestic first" seat. B6 flight 19 and 619 direct from Boston has their new lie-flat mint product.

If you want a lie-flat Transcon you have to either fly BOS-SFO on UA or B6 and connect to SAN (A route B6 does not fly!) on a non lie-flat plane OR connect via JFK/EWR and LAX and take AA, UA or B6 to LAX and connect to SAN via an express plane (Another route B6 does not fly).

The short answer is there is no tool to help with this search, but luckily the long answer is not very long: Direct on B6, connect in SFO, or double connect in NYC and LAX