You can avoid mucking about with counters and stuff by making the implicit list in the for loop an explicit array then splice chunks off it:

#!/usr/bin/perl
use warnings;
use strict;

my %accounts = (
  tom => "BigApple",
  tom2 => "BigApple2",
  tom3 => "BigApple3",
  tom4 => "BigApple4",
  tom5 => "BigApple5",
  tom6 => "BigApple6",
  tom7 => "BigApple7",
);
my @keys = reverse sort keys %accounts;

print join ("\t", @$_), "\n" while @$_ = splice @keys, 0, 3;
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Prints:

tom7    tom6    tom5
tom4    tom3    tom2
tom
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