How do I check if the user is a site owner in a network?

I have had similar issues with this in the past, WordPress really does need a is_user_admin() function.

In the meantime I think the best way to do this is to test if the user has certain capabilities.

function is_user_admin(){
    if(!is_super_admin() && current_user_can('activate_plugins'){
        // User is an admin
    }
}

Reference:

• Administrator roles
• current_user_can()