(defvar my-syntax-table (make-syntax-table))
(mapc (lambda (c) (modify-syntax-entry c "w" my-syntax-table)) '(?- ?_))
(defadvice isearch-yank-word-or-char (around skip-char-set activate)
(with-syntax-table my-syntax-table ad-do-it))

とかではどうだろう。

aaa_bbb_ccc

aaa-bbb-ccc