Download a copy of Modernizr, put it in your plugin’s directory and simply enqueue the script whenever needed. Done.
You could check whether a script was loaded by using the
wp_script_is() function. However, that function expects the name of the handle the script was registered by. You can only guess, right? Even if we assume the handle name is simply "modernizr", how do you check for a certain version (like 2.6.1)? Or worse, since custom Modernizr builds are possible, how do you check the features you need are included?
Am I missing something here or is this just the messy situation you somehow have to deal with when developing plugins?