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I tried building kinetic with python3 as well today and got the same error. After browsing https://github.com/ros/ros-overlay/issues/581#issuecomment-445942798, it seems that the boost_python3 libraries names got changed. In /usr/lib/x86_64-linux-gnu for my install of Ubuntu 16.04, the library is named libboost_python-py35.so, while it is named libboost_python3.so in the github thread. Creating a symbolic link with this latter name resolved the error for me.
cd /usr/lib/x86_64-linux-gnu
sudo ln -s libboost_python-py35.so libboost_python3.so
sudo ln -s libboost_python-py35.a libboost_python3.a
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