More than 340 people died in the disasters, prompting accusations that Boeing put profit before safety.
Families of the victims welcomed Mr Muilenberg's resignation as overdue.
But they said Boeing's decision to replace him with a long-time board member raised questions about its commitment to change.
Boeing named David Calhoun, who has served on the firm's board since 2009 and is its current chairman, as chief executive and president.
