Geoff McGrath, 49, of Seattle and 17-year-old Pascal Tessier of Kensington, Md., say donations through the AmazonSmile program should be suspended until the Boy Scouts lifts its ban on gay leaders.
They said they had 125,000 signatures gathered through Change.org in the boxes they delivered to Amazon.
Asked for comment, Amazon said: "Customers can select from nearly a million legally recognized 501(c)(3) charitable organizations on AmazonSmile. We rely on lists published by the Southern Poverty Law Center and the US Office of Foreign Assets Control to determine if certain organizations are ineligible to participate."
A small group that rallied to present the petitions carried signs that said "Exclusion is no solution" and "Amazon honor your policy, stop supporting discrimination."
In addition to Tessier and McGrath, the group included August Easton Calabria, 18, a straight Eagle Scout whose twin brother is a gay Eagle Scout, and Jesse Pacem, a straight Eagle Scout who is chapter leader of the Chief Seattle Scouts for Equality.
Each carried a box of signatures to Amazon's entrance, where Matt Oien, of the company's security department, said they would be given to the appropriate people.
Pacem spoke at the petition rally and said his first reaction to hearing that Amazon.com Inc. would be targeted was reluctance, because Amazon and its CEO, Jeff Bezos, have donated large sums of money to scouting, but then Pacem said Amazon wasn't following its own anti-discrimination guidelines.
Pascal, who earned his Eagle badge in January, started the petition on Change.org and said it took about a month to collect the 125,000 signatures.
McGrath, a Seattle software engineer who was told in March that he violated leadership qualifications, held up the three-finger Scout sign and led the group in reciting the Scout Law.