Normally one would use もらいました (as long as you are talking to some 3rd (in this case literally 4th) party not so closely associated with the boss).
(Actually, at least for people below their 50s, when telling a friend that you (yourself) have received something from your boss, if having to choose between the 2, I think もらいました would be more common, although the most natural in that case would probably be "上司は私におみやげをくれました" (or maybe 買ってくれました)
p.s. But, you might even use いただきました when talking to your friend who received the souvenir from his/her boss, if your friend had first indicated that he/she did not appreciate the souvenir, and you want to, seriously or as a joke, indicate the the boss deserves more gratitude from your friend. (ちょっとひどいね。課長からいただいたでしょう)