Beckham was selected with the No. 12 pick after excelling over three seasons at LSU. As a junior with the Tigers, he caught 57 passes for 1,117 yards and eight touchdowns.
The Eagles selected Vanderbilt product Jordan Matthews with their second-round pick after taking Louisville defensive end Marcus Smith in the first round.
"In my opinion, I thought he was the best in the draft," Kelly said. "I think he's showing people that."
Beckham, who missed the first four games of the season while battling a hamstring injury, has recorded more receiving yards (1,120) than both players and more receiving touchdowns (11) than Watkins. In addition, his 79 receptions are a Giants rookie record.
Beckham's run of eight consecutive games with at least 90 receiving yards is one short of the NFL record set by former Cowboys star Michael Irvin in 1995. Beckham also drew national attention for an incredible, one-handed touchdown catch against the Dallas Cowboys in November.
Beckham was not voted into the 2015 Pro Bowl but he was selected as a first alternate.
The Giants (6-9) host the Eagles to close the regular season on Sunday.