Well, do_action() is in plugin.php for a reason. It’s intended for use by plugins, just like apply_filters(). This function is not the cause, it is just the middleman. It’s like saying your pizza tastes bad because of the delivery guy – instead of the restaurant itself.
This is almost certainly caused by a plugin.
I suggest the plugin P3 (Plugin Performance Profiler) to analyze the performance of plugins. Some plugins are especially bloated (Jetpack, SEO Ultimate) but can be optimized by disabling unneeded modules.
https://wordpress.org/plugins/p3-profiler/
Other plugins may be available if the GoDaddy brand is not for you, I dislike GoDaddy myself, but this plugin is great.