My suggestion would be to go with the first option that Corion mentioned above: have gnuplot save its image to a file instead of opening its own display window. I gather you've had success already with using something like this:

my $chart = Chart::Gnuplot->new(
    output => 'test.png', # not "terminal => 'windows'"
    ...
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That way, gnuplot will exit as soon as the file is written, and then you just have to load the file into a new Tk::Toplevel window. I'd be inclined to make the file name different on each "plot" call - e.g. rename "test.png" to some new unique name after calling plot3d, and use the new name to label and load the new Toplevel window, like this:

my $output_id = 0;  # put this before the MainLoop call

...

sub plot {
    $chart->plot3d($dataSet);
    my $newname = sprintf( "test_%03d.png", ++$output_id );
    rename( "test.png", $newname );

    my $top = $mw->Toplevel( -title => $newname );
    my $img = $top->Photo( -file => $newname );
    my $lbl => $top->Label( -image => $img )->pack;
}
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(updated to adjust file name in second paragraph)