Every time Apple comes out with a new version of OS X, BIBINPUTS gets broken, and a new workaround has to be found. I found the following works for Yosemite, so I post here (I should I put it on a wiki)?
Mac Yosemite Adapted from: http://stackoverflow.com/questions/25385934/ yosemite-launchd-conf-no-longer-work launch AppleScript Editor, enter: do shell script "launchctl setenv setenv BIBINPUTS path(s)". Separate multiple paths with : Notice that the string after BIBINPUTS cannot contain spaces. Now save (⌘+s) as File format: Application. Finally open System Settings → Users & Groups → Login Items and add your new application. Notice that if LyX starts before the script is run, the environment will not be active. Then restart LyX.
