I think you should install the -dev package for GTK+3. On my more recent Ubuntu version the package is called libgtk-3-dev but IIRC it used to be called something else. It's the GTK+3 version of the libgtk2.0-dev one you list above.

When compiling with the official tarball, pass --enable-gtk3 to the configure script so it will fail and tell you whether you have the GTK+3 stuff installed.

Most likely when Ubuntu 16.04 was released, the Geany packages were built with GTK+2 so using commands such as apt-get build-dep geany probably won't install the GTK+3 stuff you need.

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