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'"
    ...

[download]
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;
}

[download]
(updated to adjust file name in second paragraph)

In reply to Re^3: Integrating TK and Chart::Gnuplot. by graff
in thread Integrating TK and Chart::Gnuplot. by Ppeoc

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.