it needs to work with mkv files
has to have a gui because the crops are different for each video
should be lightweight, I don't want to install premier just for this
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I don't know if it is "the best" because that is a relative term. But a great option is VirtualDub2.
It is a GUI, preview the cropped result and you can directly stream the audio so it does not recompress for example.
You can also resample the rendered video because cropping changes the dimensions of it.