Don't forget about
http://www.kayak.com which searches jetblue.com directly. It has the multiple airport option.
As for ITA, I have found that its fares are in line with jetblue.com but haven't used it too much for B6 so I can't say for sure.
expertflyer.com also has fare/inventory info available for many if not most/all routes that B6 flies on although I would expect that to be the same info that ITA has.