Starting in OS X 10.7 (Lion) the location of jni.h is different. The configure.macosx addresses this by checking for version 10.7 and adding the new location to JAVA_CPPFLAGS. However, the check currently only tests for version 10.7 when it should check for 10.7 or greater. See the exact line I'm talking about in the current head of trunk at https://github.com/apache/mesos/blob/fcc113f93113a32b26e668b7d27b1110e72a7dac/configure.macosx#L6
if test ! -z `sw_vers -productVersion | grep 10.7`; then
I believe a fix would be to have this line instead use Bash's extended test command (as suggested in the comment by user "Steev" on this blog post http://bkhome.org/blog/?viewDetailed=02199) which can compare dotted version numbers:
if [[ "$osx_version" == "10.7" || "$osx_version" > "10.7" ]]; then
At least, this seems to work for me on 10.8.1 (Mountain Lion).