You need the s modifier so that the dot matches a newline too. This regex will do it for you:

#!/usr/bin/perl -w

my $html = qq|
<!-- HTML comment#1
Some comment
-->
Some text
<!-- HTML comment#2
Some comment
-->
|;

my $comment='<!--.*?-->';
$html=~ s/$comment//sg;
print "=$html=\n";
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